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Articles

The uncharacterized Pseudomonas aeruginosa PA4189 is a novel and efficient aminoacetaldehyde dehydrogenase

Arline Fernández-Silva, Ana L. Juárez-Vázquez, Lilian González-Segura, Javier Andrés Juárez-Díaz, Rosario A. Muñoz-Clares

Biochem J (2023) 480 (4): 259–281.

DOI: https://doi.org/10.1042/BCJ20220567

Published: 23 February 2023

... 2 2 2023 © 2023 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2023 bacterial metabolism enzyme kinetics molecular docking protein crystallography site-directed mutagenesis structure–function relationships In agreement with the well...

View article titled, The uncharacterized Pseudomonas aeruginosa PA4189 is a novel and efficient aminoacetaldehyde dehydrogenase

Includes: Supplementary data

Articles

Rational design of electron/proton transfer mechanisms in the exoelectrogenic bacteria Geobacter sulfurreducens

Marta A. Silva, Pilar C. Portela, Carlos A. Salgueiro

Biochem J (2021) 478 (14): 2871–2887.

DOI: https://doi.org/10.1042/BCJ20210365

Published: 23 July 2021

... 5 2021 18 6 2021 29 6 2021 30 6 2021 © 2021 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2021 electron transfer Geobacter multiheme cytochrome c NMR spectroscopy site-directed mutagenesis Geobacter bacteria...

View article titled, Rational design of electron/proton transfer mechanisms in the exoelectrogenic bacteria Geobacter sulfurreducens

Includes: Supplementary data

Articles

Enhanced plant-microbe remediation of PCBs in soil using enzyme modification technique combined with molecular docking and molecular dynamics

Minghao Li, Wei He, Yu Li

Biochem J (2021) 478 (10): 1921–1941.

DOI: https://doi.org/10.1042/BCJ20210104

Published: 24 May 2021

.... A multifunctional plant degradation enzyme was constructed with three functional roles of absorption, degradation, and mineralization using amino acid sequence recombination and site-directed mutagenesis to modify the template of plant degradation enzyme. Finally, using the Taguchi experimental design-assisted...

View article titled, Enhanced plant-microbe remediation of PCBs in soil using enzyme modification technique combined with molecular docking and molecular dynamics

Articles

Pro4 prolyl peptide bond isomerization in human galectin-7 modulates the monomer-dimer equilibrum to affect function

Michelle C. Miller, Irina V. Nesmelova, Vladimir A. Daragan, Hans Ippel, Malwina Michalak, Aurelio Dregni, Herbert Kaltner, Jürgen Kopitz, Hans-Joachim Gabius, Kevin H. Mayo

Biochem J (2020) 477 (17): 3147–3165.

DOI: https://doi.org/10.1042/BCJ20200499

Published: 04 September 2020

... Press and the Biochemical Society. apoptosis lectin molecular dynamics NMR relaxation NMR spectroscopy site-directed mutagenesis Functionally, Gal-7 is intimately involved in growth regulation, as illustrated, for example, by the response to ectopic expression in UV-exposed...

View article titled, Pro4 prolyl peptide bond isomerization in human galectin-7 modulates the monomer-dimer equilibrum to affect function

Includes: Supplementary data

Articles

Carrot ‘antifreeze’ protein has an irregular ice-binding site that confers weak freezing point depression but strong inhibition of ice recrystallization

Yannan Wang, Laurie A. Graham, Zhifu Han, Robert Eves, Audrey K. Gruneberg, Robert L. Campbell, Heqiao Zhang, Peter L. Davies

Biochem J (2020) 477 (12): 2179–2192.

DOI: https://doi.org/10.1042/BCJ20200238

Published: 22 June 2020

.... Unexpectedly, close examination of its surface did not reveal any large regions of flat, regularly spaced hydrophobic residues that characterize the ice-binding sites (IBSs) of potent antifreeze proteins from freeze-resistant fish and insects. An IBS was defined by site-directed mutagenesis of residues...

View article titled, Carrot ‘antifreeze’ protein has an irregular ice-binding site that confers weak freezing point depression but strong inhibition of ice recrystallization

Includes: Multimedia, Supplementary data

Articles

Structural and biochemical evidence of the glucose 6-phosphate-allosteric site of maize C 4 -phosphoenolpyruvate carboxylase: its importance in the overall enzyme kinetics

Rosario A. Muñoz-Clares, Lilian González-Segura, Javier Andrés Juárez-Díaz, Carlos Mújica-Jiménez

Biochem J (2020) 477 (11): 2095–2114.

DOI: https://doi.org/10.1042/BCJ20200304

Published: 15 June 2020

...Rosario A. Muñoz-Clares; Lilian González-Segura; Javier Andrés Juárez-Díaz; Carlos Mújica-Jiménez Activation of phosphoenolpyruvate carboxylase (PEPC) enzymes by glucose 6-phosphate (G6P) and other phospho-sugars is of major physiological relevance. Previous kinetic, site-directed mutagenesis...

View article titled, Structural and biochemical evidence of the glucose 6-phosphate-allosteric site of maize C 4 -phosphoenolpyruvate carboxylase: its importance in the overall enzyme kinetics

Includes: Supplementary data

Articles

ACE-domain selectivity extends beyond direct interacting residues at the active site

Gyles E. Cozier, Lizelle Lubbe, Edward D. Sturrock, K. Ravi Acharya

Biochem J (2020) 477 (7): 1241–1259.

DOI: https://doi.org/10.1042/BCJ20200060

Published: 09 April 2020

... inhibition kinetics metalloproteases protein crystallography site-directed mutagenesis Angiotensin-converting enzyme (ACE, EC 3.4.15.1) is a zinc metalloprotease which has traditionally been known for its role in blood pressure regulation via the renin–angiotensin–aldosterone system (RAAS). During...

View article titled, ACE-domain selectivity extends beyond direct interacting residues at the active site

Articles

Insights into the biochemical and functional characterization of sortase E transpeptidase of Corynebacterium glutamicum

Aliyath Susmitha, Kesavan Madhavan Nampoothiri, Harsha Bajaj

Biochem J (2019) 476 (24): 3835–3847.

DOI: https://doi.org/10.1042/BCJ20190812

Published: 23 December 2019

... Nampoothiri ( madhavan@niist.res.in ) 5 11 2019 6 12 2019 9 12 2019 9 12 2019 © 2019 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2019 C. glutamicum class E sortase peptide cleavage site-directed mutagenesis substrate...

View article titled, Insights into the biochemical and functional characterization of sortase E transpeptidase of Corynebacterium glutamicum

Articles

Structures of c-di-GMP/cGAMP degrading phosphodiesterase Vc EAL: identification of a novel conformational switch and its implication

Malti Yadav, Kamalendu Pal, Udayaditya Sen

Biochem J (2019) 476 (21): 3333–3353.

DOI: https://doi.org/10.1042/BCJ20190399

Published: 15 November 2019

... by Portland Press Limited on behalf of the Biochemical Society 2019 c-di-GMP cGAMP crystallography phosphodiesterase second messenger site-directed mutagenesis Cyclic dinucleotides (CDNs) have been implicated in modulating varieties of cellular activities in bacteria that include motility...

View article titled, Structures of c-di-GMP/cGAMP degrading phosphodiesterase Vc EAL: identification of a novel conformational switch and its implication

Includes: Supplementary data

Articles

Plant glutathione biosynthesis revisited: redox-mediated activation of glutamylcysteine ligase does not require homo-dimerization

Yingxue Yang, Esther D. Lenherr, Roland Gromes, Shanshan Wang, Markus Wirtz, Rüdiger Hell, Tanja Peskan-Berghöfer, Klaus Scheffzek, Thomas Rausch

Biochem J (2019) 476 (7): 1191–1203.

DOI: https://doi.org/10.1042/BCJ20190072

Published: 15 April 2019

... was then mutated in amino acid residues involved in the zipper-like arrangement at the dimer interface [ 13 , 15 ]. After disrupting the dimer interface by site-directed mutagenesis, the recombinant mutant GCL proteins were analyzed for enzyme activity and dimerization state. In summary, the results reveal...

View article titled, Plant glutathione biosynthesis revisited: redox-mediated activation of glutamylcysteine ligase does not require homo-dimerization

Includes: Supplementary data

Articles

Rational engineering of a malate dehydrogenase for microbial production of 2,4-dihydroxybutyric acid via homoserine pathway

Cláudio J.R. Frazão, Christopher M. Topham, Yoann Malbert, Jean Marie François, Thomas Walther

Biochem J (2018) 475 (23): 3887–3901.

DOI: https://doi.org/10.1042/BCJ20180765

Published: 12 December 2018

... of the Biochemical Society 2018 homoserine malate dehydrogenase protein engineering site-directed mutagenesis synthetic biology A central challenge in the creation of a resource-efficient and sustainable bioeconomy lies in the reduction in our dependence on fossil resources and a shift in focus...

View article titled, Rational engineering of a malate dehydrogenase for microbial production of 2,4-dihydroxybutyric acid via homoserine pathway

Includes: Supplementary data

Articles

Identification of active site residues implies a two-step catalytic mechanism for acyl-ACP thioesterase

Fuyuan Jing, Marna D. Yandeau-Nelson, Basil J. Nikolau

Biochem J (2018) 475 (23): 3861–3873.

DOI: https://doi.org/10.1042/BCJ20180470

Published: 10 December 2018

..., mutations at specific conserved sites were generated with the QuikChange site-directed mutagenesis kit (Agilent Technologies, U.S.A.), following the manufacturer's instructions. Residues targeted for mutations were Asn321, His323, Glu357, and Cys358 in CnFatB2; Asn315, His317, Glu351, and Cys352 in CvFatB1...

View article titled, Identification of active site residues implies a two-step catalytic mechanism for acyl-ACP thioesterase

Includes: Supplementary data

Articles

A phosphatidic acid-binding protein is important for lipid homeostasis and adaptation to anaerobic biofilm conditions in Pseudomonas aeruginosa

Maike K. Groenewold, Marco Massmig, Stefanie Hebecker, Linna Danne, Zofia Magnowska, Manfred Nimtz, Franz Narberhaus, Dieter Jahn, Dirk W. Heinz, Lothar Jänsch, Jürgen Moser

Biochem J (2018) 475 (11): 1885–1907.

DOI: https://doi.org/10.1042/BCJ20180257

Published: 06 June 2018

... of phospholipid metabolism. Structure-guided site-directed mutagenesis was used to explore the proposed ligand-binding cavity of PA3911. Protein variants of Leu 56 , Leu 58 , Val 69 and Leu 114 were shown to impair PA interaction. A comparative shotgun lipidomics approach demonstrated a multifaceted response of P...

View article titled, A phosphatidic acid-binding protein is important for lipid homeostasis and adaptation to anaerobic biofilm conditions in Pseudomonas aeruginosa

Includes: Supplementary data

Articles

Identification of residues critical for proton-coupled glutathione translocation in the yeast glutathione transporter, Hgt1p

Mohammad Zulkifli, Anand Kumar Bachhawat

Biochem J (2017) 474 (11): 1807–1821.

DOI: https://doi.org/10.1042/BCJ20161063

Published: 16 May 2017

... Society 2017 oligopeptide transporter family Saccharomyces cerevisiae site-directed mutagenesis transmembrane proteins transport The electrochemical proton gradient acts as the driving force for the uptake and efflux of many metabolites and ions across the plasma membrane of fungi...

View article titled, Identification of residues critical for proton-coupled glutathione translocation in the yeast glutathione transporter, Hgt1p

Includes: Supplementary data

Articles

Hydrophobic ice-binding sites confer hyperactivity of an antifreeze protein from a snow mold fungus

Jing Cheng, Yuichi Hanada, Ai Miura, Sakae Tsuda, Hidemasa Kondo

Biochem J (2016) 473 (21): 4011–4026.

DOI: https://doi.org/10.1042/BCJ20160543

Published: 27 October 2016

.... 2 6 2016 7 9 2016 9 9 2016 9 9 2016 © 2016 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society 2016 cold adaptation crystallography ice growth inhibition molecular docking site-directed mutagenesis thermal hysteresis...

View article titled, Hydrophobic ice-binding sites confer hyperactivity of an antifreeze protein from a snow mold fungus

Articles

Substrate specificity and mapping of residues critical for transport in the high-affinity glutathione transporter Hgt1p

Mohammad Zulkifli, Shambhu Yadav, Anil Thakur, Shiffalli Singla, Monika Sharma, Anand Kumar Bachhawat

Biochem J (2016) 473 (15): 2369–2382.

DOI: https://doi.org/10.1042/BCJ20160231

Published: 28 July 2016

...-directed mutagenesis substrate specificity transmembrane domain Glutathione (γ-glutamyl- L -cysteinyl-glycine) is an essential metabolite in all unicellular and multicellular eukaryotes, barring a few amitochondrial organisms [ 1 , 2 ]. Glutathione defends against oxidative stress...

View article titled, Substrate specificity and mapping of residues critical for transport in the high-affinity glutathione transporter Hgt1p

Includes: Supplementary data

Articles

Mechanism of chitosan recognition by CBM32 carbohydrate-binding modules from a Paenibacillus sp. IK-5 chitosanase/glucanase

Shoko Shinya, Shigenori Nishimura, Yoshihito Kitaoku, Tomoyuki Numata, Hisashi Kimoto, Hideo Kusaoke, Takayuki Ohnuma, Tamo Fukamizo

Biochem J (2016) 473 (8): 1085–1095.

DOI: https://doi.org/10.1042/BCJ20160045

Published: 08 April 2016

... 2016 © 2016 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2016 CBM32 chitosan crystal structure NMR spectroscopy isothermal titration calorimetry site-directed mutagenesis Interactions between soil bacteria and fungal pathogens play...

View article titled, Mechanism of chitosan recognition by CBM32 carbohydrate-binding modules from a Paenibacillus sp. IK-5 chitosanase/glucanase

Includes: Supplementary data

Articles

A paralogue of the phosphomutase-like gene family in Candida glabrata , Cg Pmu2, gained broad-range phosphatase activity due to a small number of clustered substitutions

Kelly A. Orlando, Christine L. Iosue, Sarah G. Leone, Danielle L. Davies, Dennis D. Wykoff

Biochem J (2015) 471 (2): 187–198.

DOI: https://doi.org/10.1042/BJ20150611

Published: 02 October 2015

... phosphatase activity on Cg Pmu2 by creating fusions of sections of CgPMU2 with CgPMU1 , a paralogue with little broad range phosphatase activity. We used site-directed mutagenesis on various fusions to sequentially convert Cg Pmu1 to Cg Pmu2. Based on molecular modelling of the Pmu proteins on to a histidine...

View article titled, A paralogue of the phosphomutase-like gene family in Candida glabrata , Cg Pmu2, gained broad-range phosphatase activity due to a small number of clustered substitutions

Articles

Catalytic surface radical in dye-decolorizing peroxidase: a computational, spectroscopic and site-directed mutagenesis study

Dolores Linde, Rebecca Pogni, Marina Cañellas, Fátima Lucas, Victor Guallar, Maria Camilla Baratto, Adalgisa Sinicropi, Verónica Sáez-Jiménez, Cristina Coscolín, Antonio Romero, Francisco Javier Medrano, Francisco J. Ruiz-Dueñas, Angel T. Martínez

Biochem J (2015) 466 (2): 253–262.

DOI: https://doi.org/10.1042/BJ20141211

Published: 20 February 2015

... electron transfer from surface tryptophan residues forming radicals appears as a general mechanism for peroxidase oxidation of bulky substrates. catalytic protein radical dye-decolorizing peroxidase EPR spectroscopy molecular docking QM/MM site-directed mutagenesis DyPs (dye-decolorizing...

View article titled, Catalytic surface radical in dye-decolorizing peroxidase: a computational, spectroscopic and site-directed mutagenesis study

Includes: Supplementary data

Articles

Soya bean Gα proteins with distinct biochemical properties exhibit differential ability to complement Saccharomyces cerevisiae gpa1 mutant

Swarup Roy Choudhury, Yuqi Wang, Sona Pandey

Biochem J (2014) 461 (1): 75–85.

DOI: https://doi.org/10.1042/BJ20131341

Published: 13 June 2014

... Gα proteins of soya bean are functionally significant as observed by in vivo complementation of yeast gpa1 mutant in the pheromone-response pathway. heterotrimeric G-protein plant G-protein site-directed mutagenesis GmGα protein soya bean G-protein activity yeast complementation...

View article titled, Soya bean Gα proteins with distinct biochemical properties exhibit differential ability to complement Saccharomyces cerevisiae gpa1 mutant

Articles

Redox regulation of chloroplastic G6PDH activity by thioredoxin occurs through structural changes modifying substrate accessibility and cofactor binding

Guillaume Née, Magali Aumont-Nicaise, Mirko Zaffagnini, Sylvie Nessler, Marielle Valerio-Lepiniec, Emmanuelle Issakidis-Bourguet

Biochem J (2014) 457 (1): 117–125.

DOI: https://doi.org/10.1042/BJ20130337

Published: 10 December 2013

... binding to its active site. dithiol/disulfide interchange glucose-6-phosphate dehydrogenase redox regulation site-directed mutagenesis thioredoxin All biochemical reagents were purchased from Sigma–Aldrich, unless otherwise stated. Wild-type and mutant G6PDH1 proteins were produced...

View article titled, Redox regulation of chloroplastic G6PDH activity by thioredoxin occurs through structural changes modifying substrate accessibility and cofactor binding

Includes: Supplementary data

Articles

A key structural domain of the Candida albicans Mdr1 protein

Ajeet Mandal, Antresh Kumar, Ashutosh Singh, Andrew M. Lynn, Khyati Kapoor, Rajendra Prasad

Biochem J (2012) 445 (3): 313–322.

DOI: https://doi.org/10.1042/BJ20120190

Published: 13 July 2012

... is an antiporter with a well-conserved ‘antiporter motif’ located within TMH5 [G(×6)G(×3)GP(×2)GP(×2)G], which is necessary for its drug/proton transport activity [ 4 ]. On the basis of theoretical measurements, Kapoor et al. [ 16 ] recently subjected the protein to rational site-directed mutagenesis and confirmed...

View article titled, A key structural domain of the Candida albicans Mdr1 protein

Includes: Supplementary data

Articles

A glycosynthase derived from an inverting GH19 chitinase from the moss Bryum coronatum

Takayuki Ohnuma, Tatsuya Fukuda, Satoshi Dozen, Yuji Honda, Motomitsu Kitaoka, Tamo Fukamizo

Biochem J (2012) 444 (3): 437–443.

DOI: https://doi.org/10.1042/BJ20120036

Published: 29 May 2012

... the tertiary structure of BcChi-A using the known X-ray structure of chitinase G from Streptomyces coelicolor A3(2) (PDB code 2CJL) [ 27 ] as a template. The modelled structure of BcChi-A was used to select mutation targets for converting the enzyme into a glycosynthase. Site-directed mutagenesis...

View article titled, A glycosynthase derived from an inverting GH19 chitinase from the moss Bryum coronatum

Includes: Supplementary data

Articles

Functional mapping of the disparate activities of the yeast moonlighting protein Hal3

J. Albert Abrie, Asier González, Erick Strauss, Joaquín Ariño

Biochem J (2012) 442 (2): 357–368.

DOI: https://doi.org/10.1042/BJ20111466

Published: 13 February 2012

... cerevisiae site-directed mutagenesis The capacity of a growing number of proteins to ‘moonlight’ – that is, to develop several functions within a single polypeptide chain that often are apparently unrelated – represents a way to expand the functional capabilities of an organism in spite...

View article titled, Functional mapping of the disparate activities of the yeast moonlighting protein Hal3

Includes: Supplementary data

Articles

Hydroperoxide and peroxynitrite reductase activity of poplar thioredoxin-dependent glutathione peroxidase 5: kinetics, catalytic mechanism and oxidative inactivation

Benjamin Selles, Martin Hugo, Madia Trujillo, Vaibhav Srivastava, Gunnar Wingsle, Jean-Pierre Jacquot, Rafael Radi, Nicolas Rouhier

Biochem J (2012) 442 (2): 369–380.

DOI: https://doi.org/10.1042/BJ20111378

Published: 13 February 2012

... described previously [ 11 ]. Several variants (E79Q, D89K, F90E and Y151R) have been obtained by PCR-based site-directed mutagenesis using two complementary mutagenic primers (Supplementary Table S1 at http://www.BiochemJ.org/bj/442/bj4420369add.htm ). Culture and purification conditions were similar...

View article titled, Hydroperoxide and peroxynitrite reductase activity of poplar thioredoxin-dependent glutathione peroxidase 5: kinetics, catalytic mechanism and oxidative inactivation

Includes: Supplementary data

Articles

A novel class of PTEN protein in Arabidopsis displays unusual phosphoinositide phosphatase activity and efficiently binds phosphatidic acid

Anne Pribat, Rodnay Sormani, Mathieu Rousseau-Gueutin, Magdalena M. Julkowska, Christa Testerink, Jerôme Joubès, Michel Castroviejo, Michel Laguerre, Christian Meyer, Véronique Germain, Christophe Rothan

Biochem J (2012) 441 (1): 161–171.

DOI: https://doi.org/10.1042/BJ20110776

Published: 14 December 2011

...-bisphosphate) and PI(3,5)P 2 (phosphatidylinositol 3,5-bisphosphate). In contrast with animal PTENs, PI(3,4,5)P 3 (phosphatidylinositol 3,4,5-trisphosphate) is a poor substrate. Site-directed mutagenesis of AtPTEN2a and molecular modelling of protein–phosphoinositide interactions indicated that substitutions...

View article titled, A novel class of PTEN protein in Arabidopsis displays unusual phosphoinositide phosphatase activity and efficiently binds phosphatidic acid

Includes: Supplementary data

Articles

Probing the S1 specificity pocket of the aminopeptidases that generate antigenic peptides

Efthalia Zervoudi, Athanasios Papakyriakou, Dimitra Georgiadou, Irini Evnouchidou, Anna Gajda, Marcin Poreba, Guy S. Salvesen, Marcin Drag, Akira Hattori, Luc Swevers, Dionisios Vourloumis, Efstratios Stratikos

Biochem J (2011) 435 (2): 411–420.

DOI: https://doi.org/10.1042/BJ20102049

Published: 29 March 2011

...) affinity chromatography as previously described for ERAP1 [ 19 ]. © The Authors Journal compilation © 2011 Biochemical Society 2011 aminopeptidase antigen kinetics peptide specificity site-directed mutagenesis substrate library Cytotoxic T-lymphocytes identify infected...

View article titled, Probing the S1 specificity pocket of the aminopeptidases that generate antigenic peptides

Includes: Supplementary data

Articles

Engineering the nucleotide coenzyme specificity and sulfhydryl redox sensitivity of two stress-responsive aldehyde dehydrogenase isoenzymes of Arabidopsis thaliana

Naim Stiti, Isaac O. Adewale, Jan Petersen, Dorothea Bartels, Hans-Hubert Kirch

Biochem J (2011) 434 (3): 459–471.

DOI: https://doi.org/10.1042/BJ20101337

Published: 24 February 2011

... 2010 © The Authors Journal compilation © 2011 Biochemical Society 2011 aldehyde dehydrogenase (ALDH) coenzyme specificity enzymatic activity oxidative stress thiol regulation site-directed mutagenesis Given the high reactivity of ROS and the toxicity of the products generated...

View article titled, Engineering the nucleotide coenzyme specificity and sulfhydryl redox sensitivity of two stress-responsive aldehyde dehydrogenase isoenzymes of Arabidopsis thaliana

Includes: Supplementary data

Articles

Phosphorylation of bacterial-type phosphoenolpyruvate carboxylase at Ser 425 provides a further tier of enzyme control in developing castor oil seeds

Brendan O'Leary, Srinath K. Rao, William C. Plaxton

Biochem J (2011) 433 (1): 65–74.

DOI: https://doi.org/10.1042/BJ20101361

Published: 15 December 2010

...) and transformed into Escherichia coli [BL21-CodonPlus (DE3)-RIL] (Stratagene) and recombinantly expressed as previously described [ 24 ]. The QuikChange® II site-directed mutagenesis kit (Stratagene) was used to generate desired mutations in RcPpc4 (S425D, P426A and R760A) and AtPpc3 (R644A...

View article titled, Phosphorylation of bacterial-type phosphoenolpyruvate carboxylase at Ser 425 provides a further tier of enzyme control in developing castor oil seeds

Includes: Supplementary data

Articles

Structural insights into the catalytic mechanism of the yeast pyridoxal 5-phosphate synthase Snz1

Xuan Zhang, Yan-Bin Teng, Jian-Ping Liu, Yong-Xing He, Kang Zhou, Yuxing Chen, Cong-Zhao Zhou

Biochem J (2010) 432 (3): 445–454.

DOI: https://doi.org/10.1042/BJ20101241

Published: 25 November 2010

... Saccharomyces cerevisiae site-directed mutagenesis Compared with the extensively studied DXP-dependent pathway in Escherichia coli , the structural basis for the DXP-independent pathway is poorly understood, despite the availability of structural data on several Pdx1 enzymes. The crystal structure...

View article titled, Structural insights into the catalytic mechanism of the yeast pyridoxal 5-phosphate synthase Snz1

Includes: Supplementary data

Articles

The organophosphate-degrading enzyme from Agrobacterium radiobacter displays mechanistic flexibility for catalysis

Fernanda Ely, Kieran S. Hadler, Lawrence R. Gahan, Luke W. Guddat, David L. Ollis, Gerhard Schenk

Biochem J (2010) 432 (3): 565–573.

DOI: https://doi.org/10.1042/BJ20101054

Published: 25 November 2010

... 23 9 2010 24 9 2010 24 9 2010 © The Authors Journal compilation © 2010 Biochemical Society 2010 Agrobacterium radiobacter crystal structure hydrogen bonding OpdA organophosphate-degrading enzyme organophosphate pesticide site-directed mutagenesis The intensive...

View article titled, The organophosphate-degrading enzyme from Agrobacterium radiobacter displays mechanistic flexibility for catalysis

Articles

Structural investigation of myo -inositol dehydrogenase from Bacillus subtilis : implications for catalytic mechanism and inositol dehydrogenase subfamily classification

Karin E. van Straaten, Hongyan Zheng, David R. J. Palmer, David A. R. Sanders

Biochem J (2010) 432 (2): 237–247.

DOI: https://doi.org/10.1042/BJ20101079

Published: 12 November 2010

... Journal compilation © 2010 Biochemical Society 2010 Bacillus subtilis inositol dehydrogenase myo inositol dehydrogenase site-directed mutagenesis structural classification X-ray crystallography myo -Inositol is ubiquitous in soil and plants. Inositol derivatives and isomers...

View article titled, Structural investigation of myo -inositol dehydrogenase from Bacillus subtilis : implications for catalytic mechanism and inositol dehydrogenase subfamily classification

Includes: Supplementary data

Articles

Intermolecular phosphotransfer is crucial for efficient catalytic activity of nucleoside diphosphate kinase

Haider Hussain Dar, Pradip K. Chakraborti

Biochem J (2010) 430 (3): 539–549.

DOI: https://doi.org/10.1042/BJ20100026

Published: 27 August 2010

... phosphotransfer activity site-directed mutagenesis The autophosphorylating ability of sNDK was assessed in an in vitro assay by incubating Ni-NTA-purified protein (12.5 ng–5 μg) with [γ- 32 P]ATP in the presence of 300 μM MgCl 2 at 24 °C for 1 min. This was followed by separation of reaction products...

View article titled, Intermolecular phosphotransfer is crucial for efficient catalytic activity of nucleoside diphosphate kinase

Includes: Supplementary data

Articles

Characterization of RNase HII substrate recognition using RNase HII–argonaute chimaeric enzymes from Pyrococcus furiosus

Sayaka Kitamura, Kosuke Fujishima, Asako Sato, Daisuke Tsuchiya, Masaru Tomita, Akio Kanai

Biochem J (2010) 426 (3): 337–344.

DOI: https://doi.org/10.1042/BJ20091553

Published: 24 February 2010

... 2010 5 1 2010 5 1 2010 © The Authors Journal compilation © 2010 Biochemical Society 2010 archaeon argonaute double-stranded RNA (dsRNA) ribonuclease H RNA–DNA duplex site-directed mutagenesis RNase H (ribonuclease H) is a ubiquitous enzyme found in all three kingdoms...

View article titled, Characterization of RNase HII substrate recognition using RNase HII–argonaute chimaeric enzymes from Pyrococcus furiosus

Includes: Supplementary data

Articles

Molecular mechanism of elongation factor 1A inhibition by a Legionella pneumophila glycosyltransferase

Ramon Hurtado-Guerrero, Tal Zusman, Shalini Pathak, Adel F. M. Ibrahim, Sharon Shepherd, Alan Prescott, Gil Segal, Daan M. F. van Aalten

Biochem J (2010) 426 (3): 281–292.

DOI: https://doi.org/10.1042/BJ20091351

Published: 24 February 2010

... The structural co-ordinates reported will appear in the Protein Data Bank under accession codes 2WZF and 2WZG. elongation factor 1A (EF1A) glucosyl transferase Legionella pneumophila microinjection site-directed mutagenesis protein structure Over the past decade several studies have reported...

View article titled, Molecular mechanism of elongation factor 1A inhibition by a Legionella pneumophila glycosyltransferase

Includes: Supplementary data

Articles

Mapping of a copper-binding site on the small CP12 chloroplastic protein of Chlamydomonas reinhardtii using top-down mass spectrometry and site-directed mutagenesis

Jenny Erales, Brigitte Gontero, Julian Whitelegge, Frédéric Halgand

Biochem J (2009) 419 (1): 75–86.

DOI: https://doi.org/10.1042/BJ20082004

Published: 13 March 2009

...-binding properties, copper-IMAC experiments and site-directed mutagenesis based on computational modelling, were coupled with top-down MS [electrospray-ionization MS and MS/MS (tandem MS)]. Immobilized-copper-ion-affinity-chromatographic experiments allowed the primary characterization of the effects...

View article titled, Mapping of a copper-binding site on the small CP12 chloroplastic protein of Chlamydomonas reinhardtii using top-down mass spectrometry and site-directed mutagenesis

Includes: Supplementary data

Articles

Asp 218 participates with Asp 213 to bind a Ca 2+ atom into the S1 subsite of aminopeptidase A: a key element for substrate specificity

Cédric Claperon, Raphael Rozenfeld, Xavier Iturrioz, Nicolas Inguimbert, Mayumi Okada, Bernard Roques, Bernard Maigret, Catherine Llorens-Cortes

Biochem J (2008) 416 (1): 37–46.

DOI: https://doi.org/10.1042/BJ20080471

Published: 28 October 2008

... of this enzyme. Based on the X-ray crystal structure of LTA4H (leukotriene A4 hydrolase/aminopeptidase; EC 3.3.2.6) [ 11 ] and the functional data collected in our previous site-directed mutagenesis studies on APA [ 12 – 17 ], we built a three-dimensional model of the mouse APA ectodomain from residues 79...

View article titled, Asp 218 participates with Asp 213 to bind a Ca 2+ atom into the S1 subsite of aminopeptidase A: a key element for substrate specificity

Includes: Supplementary data

Articles

Glutamine-181 is crucial in the enzymatic activity and substrate specificity of human endoplasmic-reticulum aminopeptidase-1

Yoshikuni Goto, Hiroe Tanji, Akira Hattori, Masafumi Tsujimoto

Biochem J (2008) 416 (1): 109–116.

DOI: https://doi.org/10.1042/BJ20080965

Published: 28 October 2008

... specificity toward synthetic substrates, its substrate specificity toward natural peptides is rather broad. Because of the pathophysiological significance of ERAP-1, it is important to elucidate the molecular basis of its enzymatic action. In the present study we used site-directed mutagenesis to identify...

View article titled, Glutamine-181 is crucial in the enzymatic activity and substrate specificity of human endoplasmic-reticulum aminopeptidase-1

Articles

Dissecting isoform selectivity of PI3K inhibitors: the role of non-conserved residues in the catalytic pocket

Mark Frazzetto, Cenk Suphioglu, Jiuxiang Zhu, Oleg Schmidt-Kittler, Ian G. Jennings, Susan L. Cranmer, Shaun P. Jackson, Kenneth W. Kinzler, Bert Vogelstein, Philip E. Thompson

Biochem J (2008) 414 (3): 383–390.

DOI: https://doi.org/10.1042/BJ20080512

Published: 27 August 2008

... isoforms of PI3K (phosphoinositide 3-kinase), yet little has been revealed about the molecular basis for the observed selectivities. Using site-directed mutagenesis, we have investigated one of the areas postulated as being critical to the observed selectivity. The residues Thr 886 and Lys 890 of the PI3Kγ...

View article titled, Dissecting isoform selectivity of PI3K inhibitors: the role of non-conserved residues in the catalytic pocket

Includes: Supplementary data

Articles

Mutational analysis of the zinc- and substrate-binding sites in the CphA metallo-β-lactamase from Aeromonas hydrophila

Carine Bebrone, Christine Anne, Frédéric Kerff, Gianpiero Garau, Kris De Vriendt, Raphaël Lantin, Bart Devreese, Jozef Van Beeumen, Otto Dideberg, Jean-Marie Frère, Moreno Galleni

Biochem J (2008) 414 (1): 151–159.

DOI: https://doi.org/10.1042/BJ20080375

Published: 29 July 2008

... spectropolarimeter. The spectra were scanned at 20 °C from 200 to 250 nm (far-UV) and from 250 to 310 nm (near-UV) with 1 nm steps. The QuikChange® site-directed mutagenesis kit (Stratagene) was used to generate all the mutations. The primers designed for these experiments are listed in Supplementary Table...

View article titled, Mutational analysis of the zinc- and substrate-binding sites in the CphA metallo-β-lactamase from Aeromonas hydrophila

Includes: Supplementary data

Articles

Proximal mutations at the type 1 copper site of CotA laccase: spectroscopic, redox, kinetic and structural characterization of I494A and L386A mutants

Paulo Durão, Zhenjia Chen, Catarina S. Silva, Cláudio M. Soares, Manuela M. Pereira, Smilja Todorovic, Peter Hildebrandt, Isabel Bento, Peter F. Lindley, Lígia O. Martins

Biochem J (2008) 412 (2): 339–346.

DOI: https://doi.org/10.1042/BJ20080166

Published: 14 May 2008

.... 1 To whom correspondence should be addressed (email lmartins@itqb.unl.pt ). 21 1 2008 25 2 2008 28 2 2008 28 2 2008 © The Authors Journal compilation © 2008 Biochemical Society 2008 CotA laccase laccase multi-copper oxidase T1 copper site-directed mutagenesis...

View article titled, Proximal mutations at the type 1 copper site of CotA laccase: spectroscopic, redox, kinetic and structural characterization of I494A and L386A mutants

Includes: Supplementary data

Articles

The roles of Tyr 91 and Lys 162 in general acid–base catalysis in the pigeon NADP + -dependent malic enzyme

Cheng-Chin Kuo, Kuan-Yu Lin, Yau-Jung Hsu, Shu-Yu Lin, Yu-Tsen Lin, Gu-Gang Chang, Wei-Yuan Chou

Biochem J (2008) 411 (3): 467–473.

DOI: https://doi.org/10.1042/BJ20071278

Published: 14 April 2008

...Cheng-Chin Kuo; Kuan-Yu Lin; Yau-Jung Hsu; Shu-Yu Lin; Yu-Tsen Lin; Gu-Gang Chang; Wei-Yuan Chou The role of general acid–base catalysis in the enzymatic mechanism of NADP + -dependent malic enzyme was examined by detailed steady-state kinetic studies through site-directed mutagenesis of the Tyr 91...

View article titled, The roles of Tyr 91 and Lys 162 in general acid–base catalysis in the pigeon NADP + -dependent malic enzyme

Articles

A critical role in structure-specific DNA binding for the acetylatable lysine residues in HMGB1

René Assenberg, Michelle Webb, Edward Connolly, Katherine Stott, Matthew Watson, Josie Hobbs, Jean O. Thomas

Biochem J (2008) 411 (3): 553–561.

DOI: https://doi.org/10.1042/BJ20071613

Published: 14 April 2008

... has a particularly high affinity [ 10 , 11 ]. acetylation high mobility group (HMG) box NMR spectroscopy non-histone protein site-directed mutagenesis The results described in the present study highlight the importance of Lys 2 and Lys 11 in the interaction of the A domain of HMGB1...

View article titled, A critical role in structure-specific DNA binding for the acetylatable lysine residues in HMGB1

Articles

A conserved hydrogen-bond network in the catalytic centre of animal glutaminyl cyclases is critical for catalysis

Kai-Fa Huang, Yu-Ruei Wang, En-Cheng Chang, Tsung-Lin Chou, Andrew H.-J. Wang

Biochem J (2008) 411 (1): 181–190.

DOI: https://doi.org/10.1042/BJ20071073

Published: 13 March 2008

... the expression vector as a template, 11 human QC mutants were constructed on the basis of the protocol of the QuikChange® Site-Directed Mutagenesis Kit (Stratagene). The wild-type and mutant human QCs were expressed in Escherichia coli cells according to a previous protocol [ 16 ], but with several...

View article titled, A conserved hydrogen-bond network in the catalytic centre of animal glutaminyl cyclases is critical for catalysis

Includes: Supplementary data

Articles

Role of histidine residues in EcoP15I DNA methyltransferase activity as probed by chemical modification and site-directed mutagenesis

Prashanth S. Jois, Nagaraj Madhu, Desirazu N. Rao

Biochem J (2008) 410 (3): 543–553.

DOI: https://doi.org/10.1042/BJ20070900

Published: 27 February 2008

... the enzyme from DEPC inactivation. Site-directed mutagenesis experiments in which the 15 histidine residues in the enzyme were replaced individually with alanine corroborated the chemical modification studies and established the importance of His-335 in the methylase activity. No gross structural differences...

View article titled, Role of histidine residues in EcoP15I DNA methyltransferase activity as probed by chemical modification and site-directed mutagenesis

Articles

Insights into the structural basis of the pH-dependent dimer–tetramer equilibrium through crystallographic analysis of recombinant Diocleinae lectins

Celso S. Nagano, Juan J. Calvete, Domingo Barettino, Alicia Pérez, Benildo S. Cavada, Libia Sanz

Biochem J (2008) 409 (2): 417–428.

DOI: https://doi.org/10.1042/BJ20070942

Published: 21 December 2007

... Society 2008 dimer–tetramer equilibrium Diocleinae lectin recombinant lectin site-directed mutagenesis synthetic gene X-ray crystal structure The apparent molecular mass of the recombinant lectins in solutions of different pH were determined by analytical ultracentrifugation at 20...

View article titled, Insights into the structural basis of the pH-dependent dimer–tetramer equilibrium through crystallographic analysis of recombinant Diocleinae lectins

Articles

Molecular characterization of the thi3 gene involved in thiamine biosynthesis in Zea mays : cDNA sequence and enzymatic and structural properties of the recombinant bifunctional protein with 4-amino-5-hydroxymethyl-2-methylpyrimidine (phosphate) kinase and thiamine monophosphate synthase activities

Maria Rapala-Kozik, Mariusz Olczak, Katarzyna Ostrowska, Agata Starosta, Andrzej Kozik

Biochem J (2007) 408 (2): 149–159.

DOI: https://doi.org/10.1042/BJ20070677

Published: 14 November 2007

... roles of Gln 98 and Met 134 residues for HMP kinase activity and of Ser 444 for TMP synthase activity were experimentally confirmed by site-directed mutagenesis. 1 To whom correspondence should be addressed (email rapala@mol.uj.edu.pl ). The nucleotide sequence data reported...

View article titled, Molecular characterization of the thi3 gene involved in thiamine biosynthesis in Zea mays : cDNA sequence and enzymatic and structural properties of the recombinant bifunctional protein with 4-amino-5-hydroxymethyl-2-methylpyrimidine (phosphate) kinase and thiamine monophosphate synthase activities

Articles

Insights into polymer versus oligosaccharide synthesis: mutagenesis and mechanistic studies of a novel levansucrase from Bacillus megaterium

Arne Homann, Rebekka Biedendieck, Sven Götze, Dieter Jahn, Jürgen Seibel

Biochem J (2007) 407 (2): 189–198.

DOI: https://doi.org/10.1042/BJ20070600

Published: 25 September 2007

... was digested with NcoI and BamHI and ligated into the previously NcoI/BamHI-cut pET11d (Novagen) yielding pRBEc1. The sacB gene was mutated using the QuikChange® site-directed mutagenesis kit (Stratagene). The forward primers used to generate the mutations were as follows (the exchanged amino acids...

View article titled, Insights into polymer versus oligosaccharide synthesis: mutagenesis and mechanistic studies of a novel levansucrase from Bacillus megaterium

Articles

Enzymatic cleavage specificity of the proα1(V) chain processing analysed by site-directed mutagenesis

Christelle Bonod-Bidaud, Mickaël Beraud, Elisabeth Vaganay, Frédéric Delacoux, Bernard Font, David J. S. Hulmes, Florence Ruggiero

Biochem J (2007) 405 (2): 299–306.

DOI: https://doi.org/10.1042/BJ20070051

Published: 27 June 2007

.... extracellular matrix metalloproteinase procollagen proteolytic processing site-directed mutagenesis transient cell transfection Most extracellular matrix proteins are synthesized by cells as precursors that undergo subsequent proteolytic processing into mature and functional molecules. Among...

View article titled, Enzymatic cleavage specificity of the proα1(V) chain processing analysed by site-directed mutagenesis

Articles

The role of Tyr 605 and Ala 607 of thimet oligopeptidase and Tyr 606 and Gly 608 of neurolysin in substrate hydrolysis and inhibitor binding

Maurício F. M. Machado, Vanessa Rioli, Fernanda M. Dalio, Leandro M. Castro, Maria A. Juliano, Ivarne L. Tersariol, Emer S. Ferro, Luiz Juliano, Vitor Oliveira

Biochem J (2007) 404 (2): 279–288.

DOI: https://doi.org/10.1042/BJ20070060

Published: 14 May 2007

... be addressed (email vitor@biofis.epm.br ). 9 1 2007 19 2 2007 21 2 2007 21 2 2007 © The Authors Journal compilation © 2007 Biochemical Society 2007 neurolysin substrate and inhibitor specificity site-directed mutagenesis thimet oligopeptidase TOP (thimet...

View article titled, The role of Tyr 605 and Ala 607 of thimet oligopeptidase and Tyr 606 and Gly 608 of neurolysin in substrate hydrolysis and inhibitor binding

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