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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

Conserved L464 in p97 D1–D2 linker is critical for p97 cofactor regulated ATPase activity

Xiaoyi Zhang, Lin Gui, Shan Li, Purbasha Nandi, Rod Carlo Columbres, Daniel E. Wong, Derek R. Moen, Henry J. Lin, Po-Lin Chiu, Tsui-Fen Chou

Biochem J (2021) 478 (17): 3185–3204.

DOI: https://doi.org/10.1042/BCJ20210288

Published: 07 September 2021

... to the effect of p37. This supports that cofactor regulation by p37 and NU is affected by D1–D2 linker mutations to some extent. anti-caner cryo-electron microscopy enzyme kinetics p97/VCP To characterize the changes observed during the cofactor titrations, we measured the apparent steady-state...

View article titled, Conserved L464 in p97 D1–D2 linker is critical for p97 cofactor regulated ATPase activity

Includes: Supplementary data

Articles

Biochemical and transcript level differences between the three human phosphofructokinases show optimisation of each isoform for specific metabolic niches

Peter M. Fernandes, James Kinkead, Iain McNae, Paul A.M. Michels, Malcolm D. Walkinshaw

Biochem J (2020) 477 (22): 4425–4441.

DOI: https://doi.org/10.1042/BCJ20200656

Published: 27 November 2020

... characterise the differences between human PFK isoforms in terms of kinetic properties, sequence and structural changes, and tissue-specific transcript levels, help explain the different and specific roles played by each of the three PFK isoforms. enzyme kinetics human liver metabolism muscle...

View article titled, Biochemical and transcript level differences between the three human phosphofructokinases show optimisation of each isoform for specific metabolic niches

Includes: Supplementary data

Articles

An acidic residue buried in the dimer interface of isocitrate dehydrogenase 1 (IDH1) helps regulate catalysis and pH sensitivity

Lucas A. Luna, Zachary Lesecq, Katharine A. White, An Hoang, David A. Scott, Olga Zagnitko, Andrey A. Bobkov, Diane L. Barber, Jamie M. Schiffer, Daniel G. Isom, Christal D. Sohl

Biochem J (2020) 477 (16): 2999–3018.

DOI: https://doi.org/10.1042/BCJ20200311

Published: 21 August 2020

... 7 2020 © 2020 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2020 buried ionizable residues cancer enzyme kinetics pH regulation post-translational modification tumor metabolism Isocitrate dehydrogenase 1 (IDH1) is a highly conserved...

View article titled, An acidic residue buried in the dimer interface of isocitrate dehydrogenase 1 (IDH1) helps regulate catalysis and pH sensitivity

Includes: Supplementary data

Articles

Molecular recognition in the product site of cellobiohydrolase Cel7A regulates processive step length

Johan Pelck Olsen, Jeppe Kari, Michael Skovbo Windahl, Kim Borch, Peter Westh

Biochem J (2020) 477 (1): 99–110.

DOI: https://doi.org/10.1042/BCJ20190770

Published: 08 January 2020

.... cellobiohydrolase cellulose enzyme kinetics inhibition processivity proofreading All structures (see Figure 4 ) were prepared in PyMOL® (Schrödinger LLC, V. 2.3.0) using a crystal structure of the catalytic domain of TrCel7A in complex with a cellononaose (PDB ID: 4C4C) [ 18 ]. Each structure...

View article titled, Molecular recognition in the product site of cellobiohydrolase Cel7A regulates processive step length

Articles

Biochemical and structural characterization of murine GBP7, a guanylate binding protein with an elongated C-terminal tail

Larissa Legewie, Jennifer Loschwitz, Nora Steffens, Martin Prescher, Xue Wang, Sander H. J. Smits, Lutz Schmitt, Birgit Strodel, Daniel Degrandi, Klaus Pfeffer

Biochem J (2019) 476 (21): 3161–3182.

DOI: https://doi.org/10.1042/BCJ20190364

Published: 05 November 2019

... and, interestingly, confocal microscopy analyses reveal that the CT tail is required for recruitment of mGBP7 to the parasitophorous vacuole of Toxoplasma gondii . enzyme kinetics GTPase guanylate binding protein homology modeling molecular dynamics protein purification Correspondence: Daniel...

View article titled, Biochemical and structural characterization of murine GBP7, a guanylate binding protein with an elongated C-terminal tail

Includes: Supplementary data

Articles

A biochemical comparison of fungal GH6 cellobiohydrolases

Stefan Jarl Christensen, Kristian Bertel Rømer Mørkeberg Krogh, Nikolaj Spodsberg, Kim Borch, Peter Westh

Biochem J (2019) 476 (15): 2157–2172.

DOI: https://doi.org/10.1042/BCJ20190185

Published: 05 August 2019

... standard buffer). Correspondence: Peter Westh ( petwe@dtu.dk ) 18 3 2019 14 7 2019 16 7 2019 16 7 2019 © 2019 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2019 Cel6A cellobiohydrolases cellulose enzyme kinetics GH6...

View article titled, A biochemical comparison of fungal GH6 cellobiohydrolases

Includes: Supplementary data

Articles

Structural basis for the C-domain-selective angiotensin-converting enzyme inhibition by bradykinin-potentiating peptide b (BPPb)

Edward D. Sturrock, Lizelle Lubbe, Gyles E. Cozier, Sylva L.U. Schwager, Afolake T. Arowolo, Lauren B. Arendse, Emma Belcher, K. Ravi Acharya

Biochem J (2019) 476 (10): 1553–1570.

DOI: https://doi.org/10.1042/BCJ20190290

Published: 31 May 2019

... of the Biochemical Society 2019 bradykinin crystallography enzyme kinetics zinc metalloprotease Correspondence: Edward D. Sturrock ( edward.sturrock@uct.ac.za ) Truncated wild-type N-domain [ 25 ] and C-domain [ 26 ], C-domain mutants (S516N [ 27 ], E403R [ 26 ] and C 1–163 Ndom-ACE [ 28...

View article titled, Structural basis for the C-domain-selective angiotensin-converting enzyme inhibition by bradykinin-potentiating peptide b (BPPb)

Articles

Discerning the mechanism of action of HtrA4: a serine protease implicated in the cell death pathway

Raghupathi Kummari, Shubhankar Dutta, Lalith K. Chaganti, Kakoli Bose

Biochem J (2019) 476 (10): 1445–1463.

DOI: https://doi.org/10.1042/BCJ20190224

Published: 21 May 2019

... followed by boiling for 5 min. All reaction products were analyzed on 12% Tris–tricine gel and bands were quantified using ImageJ software (1.47V, NIH, U.S.A.). For all quantitative enzyme kinetic studies, fluorescein isothiocyanate (FITC)-labelled casein (Sigma, St. Louis, MO, U.S.A.) was used...

View article titled, Discerning the mechanism of action of HtrA4: a serine protease implicated in the cell death pathway

Includes: Supplementary data

Articles

Substrate-assisted mechanism of catalytic hydrolysis of misaminoacylated tRNA required for protein synthesis fidelity

Mykola M. Ilchenko, Mariia Yu. Rybak, Alex V. Rayevsky, Oksana P. Kovalenko, Igor Ya. Dubey, Michael A. Tukalo

Biochem J (2019) 476 (4): 719–732.

DOI: https://doi.org/10.1042/BCJ20180910

Published: 28 February 2019

...) (EC 3.1.1.96). density functional theory enzyme kinetics enzyme–substrate interactions molecular dynamics thermodynamics translation factors © 2019 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2019 30 11 2018 28 1 2019 1 2...

View article titled, Substrate-assisted mechanism of catalytic hydrolysis of misaminoacylated tRNA required for protein synthesis fidelity

Includes: Supplementary data

Articles

Rhodobacter sphaeroides methionine sulfoxide reductase P reduces R - and S -diastereomers of methionine sulfoxide from a broad-spectrum of protein substrates

Lionel Tarrago, Sandrine Grosse, Marina I. Siponen, David Lemaire, Béatrice Alonso, Guylaine Miotello, Jean Armengaud, Pascal Arnoux, David Pignol, Monique Sabaty

Biochem J (2018) 475 (23): 3779–3795.

DOI: https://doi.org/10.1042/BCJ20180706

Published: 06 December 2018

... 8 2018 26 10 2018 1 11 2018 2 11 2018 © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2018 enzyme kinetics methionine sulfoxide reductase molybdoenzyme oxidative stress protein oxidation proteomics Aerobic life...

View article titled, Rhodobacter sphaeroides methionine sulfoxide reductase P reduces R - and S -diastereomers of methionine sulfoxide from a broad-spectrum of protein substrates

Includes: Supplementary data

Articles

Inhibitor potency varies widely among tumor-relevant human isocitrate dehydrogenase 1 mutants

Diego Avellaneda Matteo, Grace A. Wells, Lucas A. Luna, Adam J. Grunseth, Olga Zagnitko, David A. Scott, An Hoang, Amit Luthra, Manal A. Swairjo, Jamie M. Schiffer, Christal D. Sohl

Biochem J (2018) 475 (20): 3221–3238.

DOI: https://doi.org/10.1042/BCJ20180424

Published: 23 October 2018

... 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2018 cancer metabolism enzyme inhibitor enzyme kinetics enzyme mutation IDH1 molecular dynamics Although alterations in tumor metabolism have been first described nearly a century ago [ 1 , 2...

View article titled, Inhibitor potency varies widely among tumor-relevant human isocitrate dehydrogenase 1 mutants

Includes: Supplementary data

Articles

Force-activated catalytic pathway accelerates bacterial adhesion against flow

Jagadish P. Hazra, Nisha Arora, Amin Sagar, Shwetha Srinivasan, Abhishek Chaudhuri, Sabyasachi Rakshit

Biochem J (2018) 475 (16): 2611–2620.

DOI: https://doi.org/10.1042/BCJ20180358

Published: 29 August 2018

... to this work. 13 5 2018 28 6 2018 2 7 2018 2 7 2018 © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2018 bacterial adhesion dynamic force spectroscopy enzyme kinetics single-molecule intermediate trapping We...

View article titled, Force-activated catalytic pathway accelerates bacterial adhesion against flow

Includes: Multimedia, Supplementary data

Articles

Role of the potassium/lysine cationic center in catalysis and functional asymmetry in membrane-bound pyrophosphatases

Erika Artukka, Heidi H. Luoto, Alexander A. Baykov, Reijo Lahti, Anssi M. Malinen

Biochem J (2018) 475 (6): 1141–1158.

DOI: https://doi.org/10.1042/BCJ20180071

Published: 26 March 2018

... Press Limited on behalf of the Biochemical Society 2018 allosteric regulation cation transporter enzyme kinetics membrane-bound pyrophosphatase protein evolution pyrophosphate 2 To evaluate the structural and functional conservation of the K + ion-binding site across...

View article titled, Role of the potassium/lysine cationic center in catalysis and functional asymmetry in membrane-bound pyrophosphatases

Articles

Structural insights into the catalytic mechanism of cysteine (hydroxyl) lyase from the hydrogen sulfide-producing oral pathogen, Fusobacterium nucleatum

Yuichiro Kezuka, Tetsuo Ishida, Yasuo Yoshida, Takamasa Nonaka

Biochem J (2018) 475 (4): 733–748.

DOI: https://doi.org/10.1042/BCJ20170838

Published: 16 February 2018

... . Correspondence: Yuichiro Kezuka ( ykezuka@iwate-med.ac.jp ) 30 10 2017 10 1 2018 16 1 2018 17 1 2018 © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2018 crystallography enzyme kinetics enzyme structure hydrogen sulfide...

View article titled, Structural insights into the catalytic mechanism of cysteine (hydroxyl) lyase from the hydrogen sulfide-producing oral pathogen, Fusobacterium nucleatum

Includes: Supplementary data

Articles

Plant DHDPR forms a dimer with unique secondary structure features that preclude higher-order assembly

Serena A.J. Watkin, Jeremy R. Keown, Eric Richards, David C. Goldstone, Sean R.A. Devenish, F. Grant Pearce

Biochem J (2018) 475 (1): 137–150.

DOI: https://doi.org/10.1042/BCJ20170709

Published: 05 January 2018

... The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2018 enzyme kinetics lysine biosynthesis oligomerisation protein evolution DHDPR enzyme activity was measured in 100 mM HEPES, pH 8.0, using a coupled assay as previously described [ 35 ]. Stock solutions...

View article titled, Plant DHDPR forms a dimer with unique secondary structure features that preclude higher-order assembly

Includes: Supplementary data

Articles

Characterization of the catalytic signature of Scabin toxin, a DNA-targeting ADP-ribosyltransferase

Bronwyn Lyons, Miguel R. Lugo, Stephanie Carlin, Taylor Lidster, A. Rod Merrill

Biochem J (2018) 475 (1): 225–245.

DOI: https://doi.org/10.1042/BCJ20170818

Published: 05 January 2018

... Merrill ( rmerrill@uoguelph.ca ) 23 10 2017 30 11 2017 4 12 2017 5 12 2017 © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2018 bacterial toxins crystallography DNA modification enzyme kinetics Pathogenic bacteria...

View article titled, Characterization of the catalytic signature of Scabin toxin, a DNA-targeting ADP-ribosyltransferase

Includes: Supplementary data

Articles

Biochemical and functional characterization of the human tissue kallikrein 9

Panagiota S. Filippou, Sofia Farkona, Davor Brinc, Yijing Yu, Ioannis Prassas, Eleftherios P. Diamandis

Biochem J (2017) 474 (14): 2417–2433.

DOI: https://doi.org/10.1042/BCJ20170174

Published: 06 July 2017

... 2017 25 5 2017 30 5 2017 30 5 2017 © 2017 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society 2017 biomarkers enzyme kinetics kallikreins proteomics serine protease inhibitors substrate specificity Kallikrein-related peptidases...

View article titled, Biochemical and functional characterization of the human tissue kallikrein 9

Includes: Supplementary data

Articles

Characterization of the activation of small GTPases by their GEFs on membranes using artificial membrane tethering

François Peurois, Simon Veyron, Yann Ferrandez, Ilham Ladid, Sarah Benabdi, Mahel Zeghouf, Gérald Peyroche, Jacqueline Cherfils

Biochem J (2017) 474 (7): 1259–1272.

DOI: https://doi.org/10.1042/BCJ20170015

Published: 23 March 2017

... ( jacqueline.cherfils@ens-paris-saclay.fr ) 9 1 2017 3 2 2017 13 2 2017 14 2 2017 © 2017 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society 2017 enzyme kinetics guanine nucleotide exchange factors membranes post-translational lipid modification...

View article titled, Characterization of the activation of small GTPases by their GEFs on membranes using artificial membrane tethering

Articles

The iron-type nitrile hydratase activator protein is a GTPase

Natalie Gumataotao, K.P. Wasantha Lankathilaka, Brian Bennett, Richard C. Holz

Biochem J (2017) 474 (2): 247–258.

DOI: https://doi.org/10.1042/BCJ20160884

Published: 06 January 2017

... 11 2016 2 11 2016 © 2017 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society 2017 enzyme kinetics metal transport nitrile hydratase protein biosynthesis Nitrile hydratases (NHases, EC 4.2.1.84) are metalloenzymes that catalyze...

View article titled, The iron-type nitrile hydratase activator protein is a GTPase

Articles

Nicotinamide N -methyltransferase catalyses the N-methylation of the endogenous β-carboline norharman: evidence for a novel detoxification pathway

Martin G. Thomas, Davide Sartini, Monica Emanuelli, Matthijs J. van Haren, Nathaniel I. Martin, David M. Mountford, David J. Barlow, Fábio Klamt, David B. Ramsden, Madeehah Reza, Richard B. Parsons

Biochem J (2016) 473 (19): 3253–3267.

DOI: https://doi.org/10.1042/BCJ20160219

Published: 27 September 2016

... liver homogenate vs. purified recombinant protein. Also, it is possible that incubation with higher concentrations of NH may yet reveal substrate inhibition. Nonetheless, these results do suggest differing regulation of NNMT's various enzyme kinetic activities, which may reflect their respective...

View article titled, Nicotinamide N -methyltransferase catalyses the N-methylation of the endogenous β-carboline norharman: evidence for a novel detoxification pathway

Includes: Supplementary data

Articles

Interdomain regulation of the ATPase activity of the ABC transporter haemolysin B from Escherichia coli

Sven Reimann, Gereon Poschmann, Kerstin Kanonenberg, Kai Stühler, Sander H.J. Smits, Lutz Schmitt

Biochem J (2016) 473 (16): 2471–2483.

DOI: https://doi.org/10.1042/BCJ20160154

Published: 11 August 2016

... enzyme kinetics haemolysin protein translocation RTX type I secretion system Type 1 secretion systems (T1SS) are membrane-embedded transport machineries involved in the secretion of a wide range of substrates in Gram-negative bacteria. Substrate transport occurs in one step from the cytosol...

View article titled, Interdomain regulation of the ATPase activity of the ABC transporter haemolysin B from Escherichia coli

Includes: Supplementary data

Articles

Releasing the brakes in coagulation Factor IXa by co-operative maturation of the substrate-binding site

Line Hyltoft Kristensen, Ole H. Olsen, Grant E. Blouse, Hans Brandstetter

Biochem J (2016) 473 (15): 2395–2411.

DOI: https://doi.org/10.1042/BCJ20160336

Published: 28 July 2016

... or hans.Brandstetter@sbg.ac.at ). 13 4 2016 25 4 2016 19 5 2016 19 5 2016 © 2016 The Author(s). published by Portland Press Limited on behalf of the Biochemical Society 2016 coagulation Factor IX conformational changes crystal structure enzyme kinetics substrate-binding site...

View article titled, Releasing the brakes in coagulation Factor IXa by co-operative maturation of the substrate-binding site

Includes: Supplementary data

Articles

Kinetic characterization and regulation of the human retinaldehyde dehydrogenase 2 enzyme during production of retinoic acid

Yehuda Shabtai, Halim Jubran, Taher Nassar, Joseph Hirschberg, Abraham Fainsod

Biochem J (2016) 473 (10): 1423–1431.

DOI: https://doi.org/10.1042/BCJ20160101

Published: 11 May 2016

... such as some forms of congenital heart disease, some types of cancer and multiple birth defects have been linked to abnormal RA signalling [ 4 – 6 ]. RA signalling regulates gene expression through the retinoic acid receptors (RARs) and retinoid X receptors (RXRs) [ 7 ]. ALDH1A2 enzyme kinetics...

View article titled, Kinetic characterization and regulation of the human retinaldehyde dehydrogenase 2 enzyme during production of retinoic acid

Includes: Supplementary data

Articles

Exploring the structure of glutamate racemase from Mycobacterium tuberculosis as a template for anti-mycobacterial drug discovery

Sinothai Poen, Yoshio Nakatani, Helen K. Opel-Reading, Moritz Lassé, Renwick C.J. Dobson, Kurt L. Krause

Biochem J (2016) 473 (9): 1267–1280.

DOI: https://doi.org/10.1042/BCJ20160186

Published: 26 April 2016

... of MurI Mtb and Mur Msm are presented in Table 1. analytical ultracentrifugation enzyme kinetics glutamate racemase monomer engineering Mycobacterium tuberculosis thermofluor Mycobacterium tuberculosis is an important pathogenic bacterium that causes tuberculosis (TB). Up...

View article titled, Exploring the structure of glutamate racemase from Mycobacterium tuberculosis as a template for anti-mycobacterial drug discovery

Includes: Supplementary data

Articles

Substrate specificity, kinetic properties and inhibition by fumonisin B 1 of ceramide synthase isoforms from Arabidopsis

Kyle D. Luttgeharm, Edgar B. Cahoon, Jonathan E. Markham

Biochem J (2016) 473 (5): 593–603.

DOI: https://doi.org/10.1042/BJ20150824

Published: 24 February 2016

... preferences and sensitivity to inhibitors and activators. Arabidopsis thaliana ceramide enzyme kinetics plant biochemistry sphingolipid 1 To whom correspondence should be addressed (email jemarkham@unl.edu ). Sphingolipids are a unique subset of membrane lipids...

View article titled, Substrate specificity, kinetic properties and inhibition by fumonisin B 1 of ceramide synthase isoforms from Arabidopsis

Includes: Supplementary data

Articles

Directed evolution of Tau class glutathione transferases reveals a site that regulates catalytic efficiency and masks co-operativity

Irine Axarli, Abdi W. Muleta, Dimitrios Vlachakis, Sophia Kossida, Georgia Kotzia, Anastasios Maltezos, Prathusha Dhavala, Anastassios C. Papageorgiou, Nikolaos E. Labrou

Biochem J (2016) 473 (5): 559–570.

DOI: https://doi.org/10.1042/BJ20150930

Published: 24 February 2016

... shuffling showed allosteric kinetics and enhanced detoxifying potential towards the herbicide fluorodifen. Its structure was determined. New engineered GSTs could be useful in biotechnology as efficient bioscavengers. allosteric regulation enzyme catalysis enzyme kinetics enzyme structure...

View article titled, Directed evolution of Tau class glutathione transferases reveals a site that regulates catalytic efficiency and masks co-operativity

Includes: Supplementary data

Articles

Incorporating covalent and allosteric effects into rate equations: the case of muscle glycogen synthase

Daniel C. Palm, Johann M. Rohwer, Jan-Hendrik S. Hofmeyr

Biochem J (2014) 462 (3): 525–537.

DOI: https://doi.org/10.1042/BJ20140196

Published: 22 August 2014

... for any particular ligand. Similarly, setting L 0 =0 or letting L 0 →∞ results in (5) (6) enzyme kinetics glycogen synthase Monod–Wyman–Changeux rate equation parameter optimization weight estimation To date a number of enzymes in pathways such as glycolysis...

View article titled, Incorporating covalent and allosteric effects into rate equations: the case of muscle glycogen synthase

Includes: Supplementary data

Articles

Multiple ecto-nucleoside triphosphate diphosphohydrolases facilitate intracellular replication of Legionella pneumophila

Patrice Riedmaier, Fiona M. Sansom, Trifina Sofian, Travis Beddoe, Ralf Schuelein, Hayley J. Newton, Elizabeth L. Hartland

Biochem J (2014) 462 (2): 279–289.

DOI: https://doi.org/10.1042/BJ20130923

Published: 07 August 2014

... secretion system. Overall our data suggest that the ability of L. pneumophila to replicate in eukaryotic cells relies in part on the ability of the pathogen to hydrolyse ATP within an intracellular compartment. ATP hydrolysis bacterial infection enzyme kinetics Legionnaire’s disease nucleoside...

View article titled, Multiple ecto-nucleoside triphosphate diphosphohydrolases facilitate intracellular replication of Legionella pneumophila

Articles

The Glu 216 /Ser 218 pocket is a major determinant of spermine oxidase substrate specificity

Manuela Cervelli, Emanuela Angelucci, Pasquale Stano, Loris Leboffe, Rodolfo Federico, Giovanni Antonini, Paolo Mariottini, Fabio Polticelli

Biochem J (2014) 461 (3): 453–459.

DOI: https://doi.org/10.1042/BJ20140305

Published: 10 July 2014

.... acetylpolyamine oxidase (APAO) enzyme catalysis enzyme kinetics polyamine spermine oxidase (SMO) substrate specificity The natural PAs (polyamines) Put (putrescine), Spd (spermidine) and Spm (spermine) are regulators of cell growth and proliferation in eukaryotic cells [ 1 – 3 ]. PA content...

View article titled, The Glu 216 /Ser 218 pocket is a major determinant of spermine oxidase substrate specificity

Articles

Characterization of the histone methyltransferase PRDM9 using biochemical, biophysical and chemical biology techniques

Xiaoying Koh-Stenta, Joma Joy, Anders Poulsen, Rong Li, Yvonne Tan, Yoonjung Shim, Jung-Hyun Min, Liling Wu, Anna Ngo, Jianhe Peng, Wei Guang Seetoh, Jing Cao, John Liang Kuan Wee, Perlyn Zekui Kwek, Alvin Hung, Umayal Lakshmanan, Horst Flotow, Ernesto Guccione, Jeffrey Hill

Biochem J (2014) 461 (2): 323–334.

DOI: https://doi.org/10.1042/BJ20140374

Published: 26 June 2014

... activities than previously recognized. biochemical characterization chemical biology enzyme kinetics epigenetics high-throughput screen histone methyltransferase PRDM protein In recent years, the PRDM family of proteins has emerged as a class of putative transcriptional regulators...

View article titled, Characterization of the histone methyltransferase PRDM9 using biochemical, biophysical and chemical biology techniques

Includes: Supplementary data

Articles

Substrate interaction dynamics and oxygen control in the active site of thymidylate synthase ThyX

Hubert F. Becker, Kamel Djaout, Isabelle Lamarre, Jonathan E. Ulmer, Delphine Schaming, Véronique Balland, Ursula Liebl, Hannu Myllykallio, Marten H. Vos

Biochem J (2014) 459 (1): 37–45.

DOI: https://doi.org/10.1042/BJ20131567

Published: 14 March 2014

...) at various dUMP concentrations. The blue open symbols in ( C ) correspond to the kinetics under the conditions of Figure 3 (NADPH mixed with the ThyX–dUMP complex), with a final dUMP concentration of 0.5 mM. enzyme kinetics flavin molecular evolution stopped flow thymidylate synthase time...

View article titled, Substrate interaction dynamics and oxygen control in the active site of thymidylate synthase ThyX

Includes: Supplementary data

Articles

Mechanistic insights into small RNA recognition and modification by the HEN1 methyltransferase

Alexandra Plotnikova, Simona Baranauskė, Aleksandr Osipenko, Saulius Klimašauskas, Giedrius Vilkaitis

Biochem J (2013) 453 (2): 281–290.

DOI: https://doi.org/10.1042/BJ20121699

Published: 28 June 2013

... recognition and modification by a representative small RNA 2′- O -methyltransferase. 12 11 2012 23 4 2013 29 4 2013 29 4 2013 © The Authors Journal compilation © 2013 Biochemical Society 2013 enzyme kinetics methyltransferase miRNA 2′- O -ribose methylation RNA...

View article titled, Mechanistic insights into small RNA recognition and modification by the HEN1 methyltransferase

Includes: Supplementary data

Articles

Effect of homomeric P450–P450 complexes on P450 function

James R. Reed, J. Patrick Connick, Dongmei Cheng, George F. Cawley, Wayne L. Backes

Biochem J (2012) 446 (3): 489–497.

DOI: https://doi.org/10.1042/BJ20120636

Published: 28 August 2012

... forms CYP1A2–CYP1A2 complexes that exhibit altered catalytic activity. © The Authors Journal compilation © 2012 Biochemical Society 2012 bioluminescence resonance energy transfer (BRET) cytochrome P450 enzyme kinetics homomeric P450–P450 complexes protein cross-linking protein–protein...

View article titled, Effect of homomeric P450–P450 complexes on P450 function

Includes: Supplementary data

Articles

Definition of the binding mode of a new class of phosphoinositide 3-kinase α-selective inhibitors using in vitro mutagenesis of non-conserved amino acids and kinetic analysis

Zhaohua Zheng, Syazwani I. Amran, Jiuxiang Zhu, Oleg Schmidt-Kittler, Kenneth W. Kinzler, Bert Vogelstein, Peter R. Shepherd, Philip E. Thompson, Ian G. Jennings

Biochem J (2012) 444 (3): 529–535.

DOI: https://doi.org/10.1042/BJ20120499

Published: 29 May 2012

.... However, in the case of p110α, this has not been possible due to the fact that the only structure of a p110α–inhibitor complex determined thus far is that of the covalently bound pan-PI3K inhibitor wortmannin [ 12 ]. In the present study we have used in vitro mutagenesis and enzyme kinetics to analyse...

View article titled, Definition of the binding mode of a new class of phosphoinositide 3-kinase α-selective inhibitors using in vitro mutagenesis of non-conserved amino acids and kinetic analysis

Includes: Supplementary data

Articles

Kinetics of Torpedo californica acetylcholinesterase inhibition by bisnorcymserine and crystal structure of the complex with its leaving group

Cecilia Bartolucci, Jure Stojan, Qian-sheng Yu, Nigel H. Greig, Doriano Lamba

Biochem J (2012) 444 (2): 269–277.

DOI: https://doi.org/10.1042/BJ20111675

Published: 11 May 2012

...) bisnorcymserine bisnoreseroline carbamate enzyme kinetics X-ray crystal structure The frequency of age-related neurodegenerative disorders and, in particular, of AD (Alzheimers's disease) is expected to greatly rise with the increasing average age of the population. AD symptoms have been associated...

View article titled, Kinetics of Torpedo californica acetylcholinesterase inhibition by bisnorcymserine and crystal structure of the complex with its leaving group

Includes: Supplementary data

Articles

Structure–function studies of a plant tyrosyl-DNA phosphodiesterase provide novel insights into DNA repair mechanisms of Arabidopsis thaliana

Hoyeun Kim, Sang Hyeon Na, So-Young Lee, Young-Min Jeong, Hyun-Ju Hwang, Jae Young Hur, Sang-Hyun Park, Je-Chang Woo, Sang-Gu Kim

Biochem J (2012) 443 (1): 49–56.

DOI: https://doi.org/10.1042/BJ20111308

Published: 14 March 2012

... TOP1–DNA complex [ 3 , 4 ]. Arabidopsis enzyme kinetics SMAD/forkheadassociated domain tyrosyl-DNA phosphodiesterase 1 (TDP1) tyrosyl-DNA phosphodiesterase (TDP) domain vanadate analogue On the basis of sequence comparison, the TDP1 protein has been shown to belong to the PLD...

View article titled, Structure–function studies of a plant tyrosyl-DNA phosphodiesterase provide novel insights into DNA repair mechanisms of Arabidopsis thaliana

Includes: Supplementary data

Articles

Plastoquinone-9 biosynthesis in cyanobacteria differs from that in plants and involves a novel 4-hydroxybenzoate solanesyltransferase

Radin Sadre, Christian Pfaff, Stephan Buchkremer

Biochem J (2012) 442 (3): 621–629.

DOI: https://doi.org/10.1042/BJ20111796

Published: 24 February 2012

... enzyme kinetics 4-hydroxybenzoate solanesyltransferase solanesyl diphosphate (SDP) plastoquinone-9 Synechocystis sp. PCC6803 PQ-9 (plastoquinone-9) represents the major prenylated quinone in organisms carrying out oxygenic photosynthesis. In plants, this lipid is synthesized at the inner...

View article titled, Plastoquinone-9 biosynthesis in cyanobacteria differs from that in plants and involves a novel 4-hydroxybenzoate solanesyltransferase

Includes: Supplementary data

Articles

Mutational analysis of allosteric activation and inhibition of glucokinase

Bogumil Zelent, Stella Odili, Carol Buettger, Dorothy K. Zelent, Pan Chen, Deborah Fenner, Joseph Bass, Charles Stanley, Monique Laberge, Jane M. Vanderkooi, Ramakanth Sarabu, Joseph Grimsby, Franz M. Matschinsky

Biochem J (2011) 440 (2): 203–215.

DOI: https://doi.org/10.1042/BJ20110440

Published: 14 November 2011

... normal GK, whereas its TF was doubled by glucose saturation. However, the enzyme kinetics, GKRP inhibition, TF enhancement by glucose and responsiveness to GKA of the selected mutants varied greatly. Two predominant response patterns were identified accounting for nearly all mutants: (i) GK mutants...

View article titled, Mutational analysis of allosteric activation and inhibition of glucokinase

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

... The Authors Journal compilation © 2010 Biochemical Society 2010 autophosphorylation bacterium enzyme kinetics NTP synthesis nucleoside diphosphate kinase phosphotransfer activity site-directed mutagenesis Restriction/modifying enzymes were obtained from New England Biolabs. All other...

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

Includes: Supplementary data

Articles

Kinetic and chemical characterization of aldehyde oxidation by fungal aryl-alcohol oxidase

Patricia Ferreira, Aitor Hernández-Ortega, Beatriz Herguedas, Jorge Rencoret, Ana Gutiérrez, María Jesús Martínez, Jesús Jiménez-Barbero, Milagros Medina, Ángel T. Martínez

Biochem J (2010) 425 (3): 585–593.

DOI: https://doi.org/10.1042/BJ20091499

Published: 15 January 2010

... The Authors Journal compilation © 2010 Biochemical Society 2010 aromatic aldehyde aryl-alcohol oxidase (AAO) enzyme kinetics gem -diol GC-MS 1 H-NMR Lignin removal is a central process for recycling of the carbon fixed by photosynthesis in land ecosystems. Lignin protects plant...

View article titled, Kinetic and chemical characterization of aldehyde oxidation by fungal aryl-alcohol oxidase

Includes: Supplementary data

Articles

Bifunctional cytosolic UDP-glucose 4-epimerases catalyse the interconversion between UDP-D-xylose and UDP-L-arabinose in plants

Toshihisa Kotake, Ryohei Takata, Rajeev Verma, Masato Takaba, Daisuke Yamaguchi, Takahiro Orita, Satoshi Kaneko, Koji Matsuoka, Tetsuo Koyama, Wolf-Dieter Reiter, Yoichi Tsumuraya

Biochem J (2009) 424 (2): 169–177.

DOI: https://doi.org/10.1042/BJ20091025

Published: 11 November 2009

... Packard). Arabidopsis bifunctionality enzyme kinetics nucleotide sugar pea ( Pisum sativum ) UDP-glucose 4-epimerase (UGE) The flux through nucleotide sugar interconversion reactions is one of the main steps controlling the amount of cell wall polysaccharides in plants [ 1 , 2...

View article titled, Bifunctional cytosolic UDP-glucose 4-epimerases catalyse the interconversion between UDP-D-xylose and UDP-L-arabinose in plants

Includes: Supplementary data

Articles

Inhibitory effects of kynurenic acid, a tryptophan metabolite, and its derivatives on cytosolic sulfotransferases

Laddawan Senggunprai, Kouichi Yoshinari, Yasushi Yamazoe

Biochem J (2009) 422 (3): 455–462.

DOI: https://doi.org/10.1042/BJ20090168

Published: 27 August 2009

... cytosolic sulfotransferase enzyme kinetics enzyme inhibition kynurenic acid tryptophan metabolism The kinetic characteristics of each mouse and human recombinant SULT were investigated with known respective substrates. The results are listed in Table 1 . All of the sulfation reactions...

View article titled, Inhibitory effects of kynurenic acid, a tryptophan metabolite, and its derivatives on cytosolic sulfotransferases

Includes: Supplementary data

Articles

Kinetic analysis of human protein arginine N-methyltransferase 2: formation of monomethyl- and asymmetric dimethyl-arginine residues on histone H4

Ted M. Lakowski, Adam Frankel

Biochem J (2009) 421 (2): 253–261.

DOI: https://doi.org/10.1042/BJ20090268

Published: 26 June 2009

... be addressed (email afrankel@interchange.ubc.ca ). 12 2 2009 6 4 2009 30 4 2009 30 4 2009 © The Authors Journal compilation © 2009 Biochemical Society 2009 co-activator enzyme kinetics histone H4 protein arginine N-methyltransferase 1 (PRMT1) protein arginine N...

View article titled, Kinetic analysis of human protein arginine N-methyltransferase 2: formation of monomethyl- and asymmetric dimethyl-arginine residues on histone H4

Includes: Supplementary data

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

... compilation © 2007 Biochemical Society 2007 cDNA cloning enzyme kinetics protein overexpression site-directed mutagenesis structural modelling thiamine phosphate diphosphorylase TDP (thiamine diphosphate) plays an essential role in all organisms as a cofactor of several universal enzymes...

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

Functional definition of the tobacco protoporphyrinogen IX oxidase substrate-binding site

Ilka U. Heinemann, Nina Diekmann, Ava Masoumi, Michael Koch, Albrecht Messerschmidt, Martina Jahn, Dieter Jahn

Biochem J (2007) 402 (3): 575–580.

DOI: https://doi.org/10.1042/BJ20061321

Published: 26 February 2007

... defects. 1 To whom correspondence should be addressed (email d.jahn@tu-bs.de ). 30 8 2006 22 11 2006 30 11 2006 30 11 2006 The Biochemical Society, London 2007 enzyme kinetics haem biosynthesis protoporphyrin protoporphyrinogen IX oxidase stopped-flow...

View article titled, Functional definition of the tobacco protoporphyrinogen IX oxidase substrate-binding site

Articles

Functional role of catalytic triad and oxyanion hole-forming residues on enzyme activity of Escherichia coli thioesterase I/protease I/phospholipase L 1

Li-Chiun Lee, Ya-Lin Lee, Ruey-Jyh Leu, Jei-Fu Shaw

Biochem J (2006) 397 (1): 69–76.

DOI: https://doi.org/10.1042/BJ20051645

Published: 14 June 2006

... as those that form a catalytic triad (Ser 10 -Asp 154 -His 157 ) and those involved in forming an oxyanion hole (Ser 10 -Gly 44 -Asn 73 ). To gain an insight into the biochemical roles of each residue, site-directed mutagenesis was employed to mutate these residues to alanine, and enzyme kinetic studies...

View article titled, Functional role of catalytic triad and oxyanion hole-forming residues on enzyme activity of Escherichia coli thioesterase I/protease I/phospholipase L 1

Articles

Characterization and selective inhibition of myristoyl-CoA:protein N -myristoyltransferase from Trypanosoma brucei and Leishmania major

Chrysoula Panethymitaki, Paul W. Bowyer, Helen P. Price, Robin J. Leatherbarrow, Katherine A. Brown, Deborah F. Smith

Biochem J (2006) 396 (2): 277–285.

DOI: https://doi.org/10.1042/BJ20051886

Published: 15 May 2006

... of fusion protein) and incubated overnight at 4 °C. 25 11 2005 10 2 2006 15 2 2006 15 2 2006 The Biochemical Society, London 2006 drug target enzyme kinetics Leishmania major myristoyl-CoA:protein N -myristoyltransferase N-myristoylation Trypanosoma brucei...

View article titled, Characterization and selective inhibition of myristoyl-CoA:protein N -myristoyltransferase from Trypanosoma brucei and Leishmania major

Articles

Probing the importance of hydrogen bonds in the active site of the subtilisin nattokinase by site-directed mutagenesis and molecular dynamics simulation

Zhong-liang Zheng, Mao-qing Ye, Zhen-yu Zuo, Zhi-gang Liu, Keng-chang Tai, Guo-lin Zou

Biochem J (2006) 395 (3): 509–515.

DOI: https://doi.org/10.1042/BJ20050772

Published: 11 April 2006

... and Thr 220 . In order to remove the effect of these hydrogen bonds, four mutants (Ser 33 →Ala 33 , Asp 60 →Ala 60 , Ser 62 →Ala 62 , and Thr 220 →Ala 220 ) were constructed by site-directed mutagenesis. The results of enzyme kinetics indicated that removal of these hydrogen bonds increases the free...

View article titled, Probing the importance of hydrogen bonds in the active site of the subtilisin nattokinase by site-directed mutagenesis and molecular dynamics simulation

Articles

Effects of novel maturity-onset diabetes of the young (MODY)-associated mutations on glucokinase activity and protein stability

María Galán, Olivier Vincent, Isabel Roncero, Sharona Azriel, Pedro Boix-Pallares, Elías Delgado-Alvarez, Francisco Díaz-Cadórniga, Enrique Blázquez, María-Angeles Navas

Biochem J (2006) 393 (1): 389–396.

DOI: https://doi.org/10.1042/BJ20051137

Published: 12 December 2005

... enzyme kinetics GCK gene glucokinase inactivating mutation maturity-onset diabetes of the young (MODY) GK (glucokinase) (ATP: D -glucose-6-phosphotransferase; EC 2.7.1.2), also known as hexokinase D or hexokinase IV, is one of the four glucose-phosphorylating isoenzymes present...

View article titled, Effects of novel maturity-onset diabetes of the young (MODY)-associated mutations on glucokinase activity and protein stability

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