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The biology and type I/III hybrid nature of type I-D CRISPR–Cas systems

Tess M. McBride, Shaharn C. Cameron, Peter C. Fineran, Robert D. Fagerlund

Biochem J (2023) 480 (7): 471–488.

DOI: https://doi.org/10.1042/BCJ20220073

Published: 13 April 2023

... 4.0 (CC BY) . bacteriophages CRISPR protein structure RNA-binding proteins Prokaryotes are under constant predation by their viruses and mobile genetic elements (MGEs), such as plasmids [ 1 ]. To counteract infection, prokaryotes have evolved an arsenal of diverse defence mechanisms...

View article titled, The biology and type I/III hybrid nature of type I-D CRISPR–Cas systems

Includes: Supplementary data

Articles

Distinct phosphorylation signals drive acceptor versus free ubiquitin chain targeting by parkin

Karen M. Dunkerley, Anne C. Rintala-Dempsey, Giulia Salzano, Roya Tadayon, Dania Hadi, Kathryn R. Barber, Helen Walden, Gary S. Shaw

Biochem J (2022) 479 (6): 751–766.

DOI: https://doi.org/10.1042/BCJ20210741

Published: 28 March 2022

... 3 2022 9 3 2022 9 3 2022 © 2022 The Author(s) 2022 This is an open access article published by Portland Press Limited on behalf of the Biochemical Society and distributed under the Creative Commons Attribution License 4.0 (CC BY) . fluorescence phosphorylation protein...

View article titled, Distinct phosphorylation signals drive acceptor versus free ubiquitin chain targeting by parkin

Includes: Supplementary data

Articles

The structure and function of modular Escherichia coli O157:H7 bacteriophage FTBEc1 endolysin, LysT84: defining a new endolysin catalytic subfamily

Michael J. Love, David Coombes, Salim Ismail, Craig Billington, Renwick C. J. Dobson

Biochem J (2022) 479 (2): 207–223.

DOI: https://doi.org/10.1042/BCJ20210701

Published: 28 January 2022

... of the Biochemical Society 2022 bacteriophages endolysin peptidoglycan hydrolase protein structure At the end of the virulent bacteriophage lytic cycle, endolysins are synthesized to degrade the peptidoglycan of the cell wall. This causes bacterial lysis to occur, releasing progeny phages from...

View article titled, The structure and function of modular Escherichia coli O157:H7 bacteriophage FTBEc1 endolysin, LysT84: defining a new endolysin catalytic subfamily

Includes: Supplementary data

Articles

Per aspera ad chaos : a personal journey to the wonderland of intrinsic disorder

Vladimir N. Uversky

Biochem J (2021) 478 (15): 3015–3024.

DOI: https://doi.org/10.1042/BCJ20210146

Published: 10 August 2021

... phenomenon in the field of macromolecular polypeptides?’ was already raised in 1995 [ 19 ]. intrinsically disordered proteins protein conformation protein structure structure–function continuum © 2021 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2021...

View article titled, Per aspera ad chaos : a personal journey to the wonderland of intrinsic disorder

Articles

C -type cytochrome-initiated reduction of bacterial lytic polysaccharide monooxygenases

Jessie Branch, Badri S. Rajagopal, Alessandro Paradisi, Nick Yates, Peter J. Lindley, Jake Smith, Kristian Hollingsworth, W. Bruce Turnbull, Bernard Henrissat, Alison Parkin, Alan Berry, Glyn R. Hemsworth

Biochem J (2021) 478 (14): 2927–2944.

DOI: https://doi.org/10.1042/BCJ20210376

Published: 28 July 2021

... License 4.0 (CC BY) . biofuels cytochrome electron transfer LPMO oxidation–reduction protein structure The production of second-generation biofuels from lignocellulosic waste in a cost-effective manner is a much-sought-after goal of the industrial biotechnology sector [ 1 , 2 ]. One...

View article titled, C -type cytochrome-initiated reduction of bacterial lytic polysaccharide monooxygenases

Includes: Supplementary data

Articles

Structures of an engineered phospholipase D with specificity for secondary alcohol transphosphatidylation: insights into plasticity of substrate binding and activation

Ariela Samantha, Jasmina Damnjanović, Yugo Iwasaki, Hideo Nakano, Alice Vrielink

Biochem J (2021) 478 (9): 1749–1767.

DOI: https://doi.org/10.1042/BCJ20210117

Published: 10 May 2021

... for this article was enabled by the participation of the University of Western Australia in an all-inclusive Read & Publish pilot with Portland Press and the Biochemical Society under a transformative agreement with CAUL. catalytic mechanism phospholipase d protein structure substrate recognition X...

View article titled, Structures of an engineered phospholipase D with specificity for secondary alcohol transphosphatidylation: insights into plasticity of substrate binding and activation

Includes: Supplementary data

Articles

Calcium binds and rigidifies the dysferlin C2A domain in a tightly coupled manner

Yuning Wang, Roya Tadayon, Liliana Santamaria, Pascal Mercier, Chantal J. Forristal, Gary S. Shaw

Biochem J (2021) 478 (1): 197–215.

DOI: https://doi.org/10.1042/BCJ20200773

Published: 15 January 2021

... ) 28 9 2020 3 12 2020 7 12 2020 7 12 2020 © 2021 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2021 calcium signaling NMR spectroscopy protein structure Muscular dystrophy is a degenerative disease that results...

View article titled, Calcium binds and rigidifies the dysferlin C2A domain in a tightly coupled manner

Articles

The Arabidopsis locus AT3G03890 encodes a dimeric β-barrel protein implicated in heme degradation

Jia Wang, Qi Guo, Xiaoyi Li, Xiao Wang, Lin Liu

Biochem J (2020) 477 (24): 4785–4796.

DOI: https://doi.org/10.1042/BCJ20200712

Published: 24 December 2020

... 2020 arabidopsis thaliana crystallography protein structure tetrapyrroles Heme is an essential pigment for plants and participates in various key biological processes [ 1 ]. It carries electrons for the respiratory and photosynthetic electron transfer chains within mitochondria...

View article titled, The Arabidopsis locus AT3G03890 encodes a dimeric β-barrel protein implicated in heme degradation

Articles

The structure of importin α and the nuclear localization peptide of ChREBP, and small compound inhibitors of ChREBP–importin α interactions

Hunmin Jung, Tomomi Takeshima, Tsutomu Nakagawa, Karen S. MacMillan, R. Max Wynn, Hanzhi Wang, Haruhiko Sakiyama, Shuguang Wei, Yang Li, Richard K. Bruick, Bruce A. Posner, Jef K. De Brabander, Kosaku Uyeda

Biochem J (2020) 477 (17): 3253–3269.

DOI: https://doi.org/10.1042/BCJ20200520

Published: 10 September 2020

...-inclusive Read & Publish pilot with Portland Press and the Biochemical Society under a transformative agreement with EBSCO. bZIP transcription factors carbohydrate binding modules carbohydrate metabolism importin alpha protein structure The liver is the primary site for de novo...

View article titled, The structure of importin α and the nuclear localization peptide of ChREBP, and small compound inhibitors of ChREBP–importin α interactions

Includes: Supplementary data

Articles

Crystal structure of a hemerythrin-like protein from Mycobacterium kansasii and homology model of the orthologous Rv2633c protein of M. tuberculosis

Zhongxin Ma, Jan Abendroth, Garry W. Buchko, Kyle H. Rohde, Victor L. Davidson

Biochem J (2020) 477 (2): 567–581.

DOI: https://doi.org/10.1042/BCJ20190827

Published: 31 January 2020

... in an all-inclusive Read & Publish pilot with Portland Press and the Biochemical Society. iron metalloprotein Mycobacterium tuberculosis protein structure The Mka HLP structure was used as a reference to construct a homology model of the Mtb HLP. This model revealed...

View article titled, Crystal structure of a hemerythrin-like protein from Mycobacterium kansasii and homology model of the orthologous Rv2633c protein of M. tuberculosis

Articles

Comparative structure, dynamics and evolution of acyl-carrier proteins from Borrelia burgdorferi , Brucella melitensis and Rickettsia prowazekii

Ravi P. Barnwal, Mandeep Kaur, Alec Heckert, Janeka Gartia, Gabriele Varani

Biochem J (2020) 477 (2): 491–508.

DOI: https://doi.org/10.1042/BCJ20190797

Published: 31 January 2020

... protein structure Acyl carrier proteins (ACPs) participate in the biosynthesis of fatty acids (FA) and polyketides by tethering intermediates to the enzyme complex [ 1 , 2 ]. In yeast and mammals, ACP is a component of fatty acid synthase, a multifunctional enzyme complex, whereas in bacteria, ACP...

View article titled, Comparative structure, dynamics and evolution of acyl-carrier proteins from Borrelia burgdorferi , Brucella melitensis and Rickettsia prowazekii

Includes: Supplementary data

Articles

Prevotella intermedia produces two proteins homologous to Porphyromonas gingivalis HmuY but with different heme coordination mode

Marcin Bielecki, Svetlana Antonyuk, Richard W. Strange, Klaudia Siemińska, John W. Smalley, Paweł Mackiewicz, Michał Śmiga, Megan Cowan, Michael J. Capper, Paulina Ślęzak, Mariusz Olczak, Teresa Olczak

Biochem J (2020) 477 (2): 381–405.

DOI: https://doi.org/10.1042/BCJ20190607

Published: 30 January 2020

... Press Limited on behalf of the Biochemical Society 2020 heme hemophore HmuY porphyromonas gingivalis prevotella intermedia protein structure Periodontal diseases belong to a group of infectious disorders, which are caused by an ecological shift in the microbial composition in the oral...

View article titled, Prevotella intermedia produces two proteins homologous to Porphyromonas gingivalis HmuY but with different heme coordination mode

Includes: Supplementary data

Articles

Two distinct nucleic acid binding surfaces of Cdc5 regulate development

Chao Wang, Mu Li, Guorui Li, Xinsen Liu, Wensheng Zhao, Bin Yu, Junfeng Liu, Jun Yang, You-Liang Peng

Biochem J (2019) 476 (21): 3355–3368.

DOI: https://doi.org/10.1042/BCJ20190502

Published: 15 November 2019

... selected for co-occurrence analysis with a confidence interval of over 95% [ 38 ]. Circular dichroism (CD) analysis was performed on a Chirascan-plus spectropolarimeter (Applied Photophysics, Leatherhead, U.K.) to estimate the protein structure at room temperature. Proteins were prepared...

View article titled, Two distinct nucleic acid binding surfaces of Cdc5 regulate development

Includes: Supplementary data

Articles

Molecular dynamics of C99-bound γ-secretase reveal two binding modes with distinct compactness, stability, and active-site retention: implications for Aβ production

Budheswar Dehury, Ning Tang, Kasper P. Kepp

Biochem J (2019) 476 (7): 1173–1189.

DOI: https://doi.org/10.1042/BCJ20190023

Published: 15 April 2019

... Alzheimer's disease amyloid beta computational biochemistry protein structure The 99-residue C-terminal fragment (C99) of the amyloid precursor protein (APP) is produced upon cleavage by β-secretase; C99 is subsequently cleaved by the enzyme-complex γ-secretase, releasing the infamous amyloid-β...

View article titled, Molecular dynamics of C99-bound γ-secretase reveal two binding modes with distinct compactness, stability, and active-site retention: implications for Aβ production

Includes: Supplementary data

Articles

Structure of SPH (self-incompatibility protein homologue) proteins: a widespread family of small, highly stable, secreted proteins

Karthik V. Rajasekar, Shuangxi Ji, Rachel J. Coulthard, Jon P. Ride, Gillian L. Reynolds, Peter J. Winn, Michael J. Wheeler, Eva I. Hyde, Lorna J. Smith

Biochem J (2019) 476 (5): 809–826.

DOI: https://doi.org/10.1042/BCJ20180828

Published: 12 March 2019

... Commons Attribution License 4.0 (CC BY) . disulfide bonds molecular modelling NMR spectroscopy plant proteins protein structure Correspondence: Eva I. Hyde ( e.i.hyde@bham.ac.uk ) or Lorna J. Smith ( lorna.smith@chem.ox.ac.uk ) * Present address: Shuangxi Ji, 56 Fuhong Road...

View article titled, Structure of SPH (self-incompatibility protein homologue) proteins: a widespread family of small, highly stable, secreted proteins

Articles

Structural and ligand-binding analysis of the YAP-binding domain of transcription factor TEAD4

Yan Li, Shuang Liu, Elizabeth Yihui Ng, Rong Li, Anders Poulsen, Jeffrey Hill, Ajaybabu V. Pobbati, Alvin W. Hung, Wanjin Hong, Thomas H. Keller, CongBao Kang

Biochem J (2018) 475 (12): 2043–2055.

DOI: https://doi.org/10.1042/BCJ20180225

Published: 26 June 2018

..., Oxford OX1 3TA, U.K. 17 3 2018 7 5 2018 10 5 2018 14 5 2018 © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2018 drug discovery and design NMR spectroscopy palmitoylation protein structure protein–protein Introduction...

View article titled, Structural and ligand-binding analysis of the YAP-binding domain of transcription factor TEAD4

Includes: Supplementary data

Articles

A plasmid borne, functionally novel glycoside hydrolase family 30 subfamily 8 endoxylanase from solventogenic Clostridium

Franz J. St John, Diane Dietrich, Casey Crooks, Peter Balogun, Vesna de Serrano, Edwin Pozharski, James Kennon Smith, Elizabeth Bales, Jason Hurlbert

Biochem J (2018) 475 (9): 1533–1551.

DOI: https://doi.org/10.1042/BCJ20180050

Published: 04 May 2018

... This is an open access article published by Portland Press Limited on behalf of the Biochemical Society and distributed under the Creative Commons Attribution License 4.0 (CC BY-NC-ND) . arabinoxylan GH30 glycoside hydrolase family 30 protein structure structure–function Enzymes of glycoside...

View article titled, A plasmid borne, functionally novel glycoside hydrolase family 30 subfamily 8 endoxylanase from solventogenic Clostridium

Includes: Supplementary data

Articles

The stress sigma factor of RNA polymerase RpoS/σ S is a solvent-exposed open molecule in solution

Paola Cavaliere, Sébastien Brier, Petr Filipenko, Christina Sizun, Bertrand Raynal, Françoise Bonneté, Fabienne Levi-Acobas, Jacques Bellalou, Patrick England, Julia Chamot-Rooke, Claudine Mayer, Françoise Norel

Biochem J (2018) 475 (1): 341–354.

DOI: https://doi.org/10.1042/BCJ20170768

Published: 15 January 2018

... length of the cell in cm. The percentage of secondary structure was obtained using Dichroweb ( http://dichroweb.cryst.bbk.ac.uk/html/home.shtml ). protein conformation protein structure RNA polymerase RpoS Salmonella sigma factor The ability to adapt quickly to variations...

View article titled, The stress sigma factor of RNA polymerase RpoS/σ S is a solvent-exposed open molecule in solution

Includes: Supplementary data

Articles

A dimeric catalytic core relates the short and long forms of ATP-phosphoribosyltransferase

Gerd Mittelstädt, Wanting Jiao, Emma K. Livingstone, Gert-Jan Moggré, Ali Reza Nazmi, Emily J. Parker

Biochem J (2018) 475 (1): 247–260.

DOI: https://doi.org/10.1042/BCJ20170762

Published: 05 January 2018

... address: Biotransformation, Scion, Rotorua 3020, New Zealand. 7 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 allosteric regulation phosphoribosyltransferase protein structure...

View article titled, A dimeric catalytic core relates the short and long forms of ATP-phosphoribosyltransferase

Articles

Role of glycosylation in nucleating protein folding and stability

Nisha Grandhi Jayaprakash, Avadhesha Surolia

Biochem J (2017) 474 (14): 2333–2347.

DOI: https://doi.org/10.1042/BCJ20170111

Published: 03 July 2017

...); published by Portland Press Limited on behalf of the Biochemical Society 2017 glycosylation protein function protein stability protein structure Glycosylation is the covalent addition of sugar moieties to the protein co-translationally or as a post-translational modification...

View article titled, Role of glycosylation in nucleating protein folding and stability

Articles

Comparative functional analysis of ribonuclease 1 homologs: molecular insights into evolving vertebrate physiology

Jo E. Lomax, Chelcie H. Eller, Ronald T. Raines

Biochem J (2017) 474 (13): 2219–2233.

DOI: https://doi.org/10.1042/BCJ20170173

Published: 21 June 2017

... ) * These authors contributed equally to this work. 3 3 2017 30 4 2017 10 5 2017 11 5 2017 © 2017 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society 2017 enzyme activity enzymology molecular evolution protein structure ribonuclease RNA...

View article titled, Comparative functional analysis of ribonuclease 1 homologs: molecular insights into evolving vertebrate physiology

Includes: Supplementary data

Articles

Ligand-induced activation of human TRPM2 requires the terminal ribose of ADPR and involves Arg1433 and Tyr1349

Ralf Fliegert, Joanna M. Watt, Anja Schöbel, Monika D. Rozewitz, Christelle Moreau, Tanja Kirchberger, Mark P. Thomas, Wiebke Sick, Andrea C. Araujo, Angelika Harneit, Barry V.L. Potter, Andreas H. Guse

Biochem J (2017) 474 (13): 2159–2175.

DOI: https://doi.org/10.1042/BCJ20170091

Published: 16 June 2017

... into the other. The second is to dock ADPR into the binding site computationally. adenosine diphosphate ribose protein structure transient receptor potential channels The presence of adenosine 5′-diphosphoribose (ADPR) in mammalian cells has been known for a long time ([ 1 ] and references therein...

View article titled, Ligand-induced activation of human TRPM2 requires the terminal ribose of ADPR and involves Arg1433 and Tyr1349

Includes: Supplementary data

Articles

Neisseria meningitidis factor H-binding protein bound to monoclonal antibody JAR5: implications for antibody synergy

Enrico Malito, Paola Lo Surdo, Daniele Veggi, Laura Santini, Heather Stefek, Brunella Brunelli, Enrico Luzzi, Matthew J. Bottomley, Peter T. Beernink, Maria Scarselli

Biochem J (2016) 473 (24): 4699–4713.

DOI: https://doi.org/10.1042/BCJ20160806

Published: 09 December 2016

... ) 29 8 2016 19 10 2016 25 10 2016 26 10 2016 © 2016 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society 2016 fHbp monoclonal antibodies Neisseria protein structure fHbp proteins were dialyzed against PBS overnight at 4°C...

View article titled, Neisseria meningitidis factor H-binding protein bound to monoclonal antibody JAR5: implications for antibody synergy

Includes: Supplementary data

Articles

Molecular basis of the osmolyte effect on protein stability: a lesson from the mechanical unfolding of lysozyme

Beata Adamczak, Miłosz Wieczór, Mateusz Kogut, Janusz Stangret, Jacek Czub

Biochem J (2016) 473 (20): 3705–3724.

DOI: https://doi.org/10.1042/BCJ20160604

Published: 11 October 2016

... folding protein structure solvation During the enforced unfolding, R gyr was changed from the initial value of 1.4 nm in the native state up to 3.0 nm, with a harmonic force constant of 7000 kJ mol –1 nm –2 , and four pulling speeds were used: 1 × 10 −4 , 1 × 10 −5 , 5 × 10 −5 and 5 × 10 −6...

View article titled, Molecular basis of the osmolyte effect on protein stability: a lesson from the mechanical unfolding of lysozyme

Includes: Supplementary data

Articles

cAMP-dependent protein kinase (PKA) complexes probed by complementary differential scanning fluorimetry and ion mobility–mass spectrometry

Dominic P. Byrne, Matthias Vonderach, Samantha Ferries, Philip J. Brownridge, Claire E. Eyers, Patrick A. Eyers

Biochem J (2016) 473 (19): 3159–3175.

DOI: https://doi.org/10.1042/BCJ20160648

Published: 27 September 2016

... kinase A protein structure Protein phosphorylation is a reversible post-translational modification (PTM) catalyzed by the protein kinase-mediated enzymatic transfer of ATP γ-phosphate to an appropriate side chain in a substrate [ 1 ]. A plethora of techniques, including X-ray crystallography...

View article titled, cAMP-dependent protein kinase (PKA) complexes probed by complementary differential scanning fluorimetry and ion mobility–mass spectrometry

Includes: Supplementary data

Articles

Structural characterization suggests models for monomeric and dimeric forms of full-length ezrin

Juanita M. Phang, Stephen J. Harrop, Anthony P. Duff, Anna V. Sokolova, Ben Crossett, James C. Walsh, Simone A. Beckham, Cuong D. Nguyen, Roberta B. Davies, Carina Glöckner, Elizabeth H.C. Bromley, Krystyna E. Wilk, Paul M.G. Curmi

Biochem J (2016) 473 (18): 2763–2782.

DOI: https://doi.org/10.1042/BCJ20160541

Published: 12 September 2016

... 2016 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society 2016 crystallography ezrin FERM domain protein dynamics protein structure small-angle scattering The ezrin, radixin, and moesin (ERM) proteins connect cell membranes and the underlying actin...

View article titled, Structural characterization suggests models for monomeric and dimeric forms of full-length ezrin

Includes: Supplementary data

Articles

Structural plasticity and in vivo activity of Cas1 from the type I-F CRISPR–Cas system

Max E. Wilkinson, Yoshio Nakatani, Raymond H.J. Staals, Sebastian N. Kieper, Helen K. Opel-Reading, Rebecca E. McKenzie, Peter C. Fineran, Kurt L. Krause

Biochem J (2016) 473 (8): 1063–1072.

DOI: https://doi.org/10.1042/BCJ20160078

Published: 08 April 2016

... prokaryotes against foreign DNA. In a type I-F CRISPR–Cas system we show that Cas1 is required for adaptation to new threats, and that this protein is characterized by remarkable structural plasticity. adaptation bacteriophages Csy horizontal gene transfer plasmids protein structure...

View article titled, Structural plasticity and in vivo activity of Cas1 from the type I-F CRISPR–Cas system

Includes: Supplementary data

Articles

Diversity in the structures and ligand-binding sites of nematode fatty acid and retinol-binding proteins revealed by Na-FAR-1 from Necator americanus

M. Florencia Rey-Burusco, Marina Ibáñez-Shimabukuro, Mads Gabrielsen, Gisela R. Franchini, Andrew J. Roe, Kate Griffiths, Bin Zhan, Alan Cooper, Malcolm W. Kennedy, Betina Córsico, Brian O. Smith

Biochem J (2015) 471 (3): 403–414.

DOI: https://doi.org/10.1042/BJ20150068

Published: 16 October 2015

... nuclear magnetic resonance (NMR) parasite protein structure retinol-binding protein X-ray 1 Correspondence may be addressed to either of these authors (email Brian.Smith@glasgow.ac.uk or malcolm.kennedy@glasgow.ac.uk ). The structures of Na-FAR-1 determined by NMR and X-ray have...

View article titled, Diversity in the structures and ligand-binding sites of nematode fatty acid and retinol-binding proteins revealed by Na-FAR-1 from Necator americanus

Includes: Supplementary data

Articles

Comparative structural analysis of the caspase family with other clan CD cysteine peptidases

Karen McLuskey, Jeremy C. Mottram

Biochem J (2015) 466 (2): 219–232.

DOI: https://doi.org/10.1042/BJ20141324

Published: 20 February 2015

...-BY) ( http://creativecommons.org/licenses/by/3.0/ ) which permits unrestricted use, distribution and reproduction in any medium, provided the original work is properly cited. caspase clan CD crystallography metacaspase peptidase protein structure Clan CD [ 1 ] cysteine peptidases use...

View article titled, Comparative structural analysis of the caspase family with other clan CD cysteine peptidases

Includes: Supplementary data

Articles

Conserved structure and domain organization among bacterial Slc26 transporters

Emma L. R. Compton, Kimberly Page, Heather E. Findlay, Michael Haertlein, Martine Moulin, Ulrich Zachariae, David G. Norman, Frank Gabel, Arnaud Javelle

Biochem J (2014) 463 (2): 297–307.

DOI: https://doi.org/10.1042/BJ20130619

Published: 22 September 2014

... that corresponded to approximately 100% 2 H 2 O. For SANS experiments, 11% 2 H 2 O was included in the gel filtration buffer and the purified proteins were concentrated with a Centricon 50-K (Millipore) to 5 mg/ml and dialysed against the same buffer. membrane protein protein purification protein structure...

View article titled, Conserved structure and domain organization among bacterial Slc26 transporters

Includes: Supplementary data

Articles

Structure of cyclin G-associated kinase (GAK) trapped in different conformations using nanobodies

Apirat Chaikuad, Tracy Keates, Cécile Vincke, Melanie Kaufholz, Michael Zenn, Bastian Zimmermann, Carlos Gutiérrez, Rong-guang Zhang, Catherine Hatzos-Skintges, Andrzej Joachimiak, Serge Muyldermans, Friedrich W. Herberg, Stefan Knapp, Susanne Müller

Biochem J (2014) 459 (1): 59–69.

DOI: https://doi.org/10.1042/BJ20131399

Published: 14 March 2014

... (nanobodies) revealed the domain plasticity of this kinase and unusual activation segment architecture. activation loop cyclin G-associated kinase drug side effect kinase inhibitor nanobody protein structure 1 These authors contributed equally to the work. 2 To whom...

View article titled, Structure of cyclin G-associated kinase (GAK) trapped in different conformations using nanobodies

Includes: Supplementary data

Articles

RipD (Rv1566c) from Mycobacterium tuberculosis : adaptation of an NlpC/p60 domain to a non-catalytic peptidoglycan-binding function

Dominic Böth, Eva Maria Steiner, Atsushi Izumi, Gunter Schneider, Robert Schnell

Biochem J (2014) 457 (1): 33–41.

DOI: https://doi.org/10.1042/BJ20131227

Published: 10 December 2013

... tuberculosis NlpC/p60 peptidoglycan binding proline-rich protein repeat protein structure The cell wall of Mycobacterium tuberculosis has a unique architecture that functions as a powerful barrier against physical and chemical stress [ 1 ]. In the outer layer of the cell envelope, complex...

View article titled, RipD (Rv1566c) from Mycobacterium tuberculosis : adaptation of an NlpC/p60 domain to a non-catalytic peptidoglycan-binding function

Includes: Supplementary data

Articles

CRISPR interference: a structural perspective

Judith Reeks, James H. Naismith, Malcolm F. White

Biochem J (2013) 453 (2): 155–166.

DOI: https://doi.org/10.1042/BJ20130316

Published: 28 June 2013

... (CRISPR) crystallography evolution protein structure repeat-associated mysterious protein (RAMP) CRISPRs (cluster of regularly interspaced palindromic repeats) are a prokaryotic defence mechanism against viral infection and horizontal gene transfer. CRISPRs are the largest family...

View article titled, CRISPR interference: a structural perspective

Includes: Supplementary data

Articles

Molecular orientation of Factor VIIIa on the phospholipid membrane surface determined by fluorescence resonance energy transfer

Hironao Wakabayashi, Philip J. Fay

Biochem J (2013) 452 (2): 293–301.

DOI: https://doi.org/10.1042/BJ20130025

Published: 10 May 2013

... coagulation Factor VIII fluorescence resonance energy transfer (FRET) phospholipid membrane protein structure F (Factor) VIII is a plasma protein that is decreased or defective in individuals with haemophilia A. FVIII circulates as a heterodimer consisting of a HC (heavy chain) comprised of A1, A2...

View article titled, Molecular orientation of Factor VIIIa on the phospholipid membrane surface determined by fluorescence resonance energy transfer

Articles

Proteomic analysis and molecular modelling characterize the iron-regulatory protein haemojuvelin/repulsive guidance molecule c

Mahta Nili, Larry David, Johannes Elferich, Ujwal Shinde, Peter Rotwein

Biochem J (2013) 452 (1): 87–95.

DOI: https://doi.org/10.1042/BJ20121845

Published: 25 April 2013

... in proteins. disulfide bond haemojuvelin iron metabolism mass spectrometry molecular modelling protein structure repulsive guidance molecule 1 To whom correspondence should be addressed (email rotweinp@ohsu.edu ). 7 12 2012 18 2 2013 6 3 2013 6 3 2013 ©...

View article titled, Proteomic analysis and molecular modelling characterize the iron-regulatory protein haemojuvelin/repulsive guidance molecule c

Includes: Supplementary data

Articles

MpaA is a murein-tripeptide-specific zinc carboxypeptidase that functions as part of a catabolic pathway for peptidoglycan-derived peptides in γ-proteobacteria

Abbas Maqbool, Mireille Hervé, Dominique Mengin-Lecreulx, Anthony J. Wilkinson, Gavin H. Thomas

Biochem J (2012) 448 (3): 329–341.

DOI: https://doi.org/10.1042/BJ20121164

Published: 21 November 2012

... for Ec_ MpaA and Vh_ MpaA respectively. E. coli MppA was purified as described previously [ 15 ]. Escherichia coli murein tripeptide protein structure transporter Vibrio harveyi zinc carboxypeptidase Peptidoglycan (murein) is the major structural component of bacterial cell...

View article titled, MpaA is a murein-tripeptide-specific zinc carboxypeptidase that functions as part of a catabolic pathway for peptidoglycan-derived peptides in γ-proteobacteria

Includes: Supplementary data

Articles

Human YKL-39 is a pseudo-chitinase with retained chitooligosaccharide-binding properties

Marianne Schimpl, Christina L. Rush, Marie Betou, Ian M. Eggleston, Anneliese D. Recklies, Daan M. F. van Aalten

Biochem J (2012) 446 (1): 149–157.

DOI: https://doi.org/10.1042/BJ20120377

Published: 27 July 2012

... chitinase-like proteins glycan glycan array glycobiology protein structure lectin X-ray crystallography The human genome possesses two genes coding for active chitinases, hCHT (chitotriosidase) and the hAMCase (acidic mammalian chitinase), both from the CAZy GH18 (glycoside hydrolase 18...

View article titled, Human YKL-39 is a pseudo-chitinase with retained chitooligosaccharide-binding properties

Articles

A urea channel from Bacillus cereus reveals a novel hexameric structure

Gerard H. M. Huysmans, Nathan Chan, Jocelyn M. Baldwin, Vincent L. G. Postis, Svetomir B. Tzokov, Sarah E. Deacon, Sylvia Y. M. Yao, James D. Young, Michael J. McPherson, Per A. Bullough, Stephen A. Baldwin

Biochem J (2012) 445 (2): 157–166.

DOI: https://doi.org/10.1042/BJ20120169

Published: 27 June 2012

... ]. cryo-electron microscopy electron crystallography Helicobacter pylori membrane protein structure urea channel Urea is used as a nitrogen source by bacteria, fungi and plants, and is the most widely used agricultural nitrogen-containing fertilizer. In vertebrates, it also plays a critical...

View article titled, A urea channel from Bacillus cereus reveals a novel hexameric structure

Includes: Supplementary data

Articles

A common structural blueprint for plant UDP-sugar-producing pyrophosphorylases

Leszek A. Kleczkowski, Matt Geisler, Elisabeth Fitzek, Malgorzata Wilczynska

Biochem J (2011) 439 (3): 375–381.

DOI: https://doi.org/10.1042/BJ20110730

Published: 13 October 2011

...-analogues, e.g. UDP-Gal (via UDP-Glc epimerase) or UDP-GlcA (via UDP-Glc dehydrogenase) [ 1 – 4 ] (where Gal is galactose and GlcA is glucuronic acid). oligomerization protein structure sugar activation UDP-sugar synthesis © The Authors Journal compilation © 2011 Biochemical Society 2011...

View article titled, A common structural blueprint for plant UDP-sugar-producing pyrophosphorylases

Includes: Supplementary data

Articles

Crystal structure of a novel type of odorant-binding protein from Anopheles gambiae , belonging to the C-plus class

Amandine Lagarde, Silvia Spinelli, Huili Qiao, Mariella Tegoni, Paolo Pelosi, Christian Cambillau

Biochem J (2011) 437 (3): 423–430.

DOI: https://doi.org/10.1042/BJ20110522

Published: 13 July 2011

... accession code 3PM2. 22 3 2011 11 5 2011 12 5 2011 12 5 2011 © The Authors Journal compilation © 2011 Biochemical Society 2011 Anopheles gambiae C-plus class odorant-binding protein odorant transport olfactory protein protein structure Olfaction is a finely...

View article titled, Crystal structure of a novel type of odorant-binding protein from Anopheles gambiae , belonging to the C-plus class

Includes: Multimedia, Supplementary data

Articles

Structure and activity of the Saccharomyces cerevisiae dUTP pyrophosphatase DUT1, an essential housekeeping enzyme

Anatoli Tchigvintsev, Alexander U. Singer, Robert Flick, Pierre Petit, Greg Brown, Elena Evdokimova, Alexei Savchenko, Alexander F. Yakunin

Biochem J (2011) 437 (2): 243–253.

DOI: https://doi.org/10.1042/BJ20110304

Published: 28 June 2011

.... 22 2 2011 4 5 2011 6 5 2011 6 5 2011 © The Authors Journal compilation © 2011 Biochemical Society 2011 dITP dUTP dUTP pyrophosphatase (dUTPase) enzyme co-operativity mutagenesis protein structure HPLC analysis of the DUT1 reaction products was performed...

View article titled, Structure and activity of the Saccharomyces cerevisiae dUTP pyrophosphatase DUT1, an essential housekeeping enzyme

Includes: Multimedia, Supplementary data

Articles

Human mitochondrial import receptor Tom70 functions as a monomer

Anna C. Y. Fan, Lisandra M. Gava, Carlos H. I. Ramos, Jason C. Young

Biochem J (2010) 429 (3): 553–563.

DOI: https://doi.org/10.1042/BJ20091855

Published: 14 July 2010

.... 1 To whom correspondence should be addressed (email jason.young2@mcgill.ca ). 7 12 2009 16 5 2010 26 5 2010 26 5 2010 © The Authors Journal compilation © 2010 Biochemical Society 2010 chaperone dimerization heat-shock protein (Hsp) mitochondrion protein...

View article titled, Human mitochondrial import receptor Tom70 functions as a monomer

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

...) glucosyl transferase Legionella pneumophila microinjection site-directed mutagenesis protein structure Over the past decade several studies have reported fascinating examples of pathogenic bacteria employing glycosyltransferases secreted into the human cell to control specific signal...

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

Includes: Supplementary data

Articles

The presence of monoglucosylated N196-glycan is important for the structural stability of storage protein, arylphorin

Kyoung-Seok Ryu, Jie-Oh Lee, Taek Hun Kwon, Han-Ho Choi, Hong-Seog Park, Soo Kyung Hwang, Zee-Won Lee, Kyung-Bok Lee, Young Hyun Han, Yun-Seok Choi, Young Ho Jeon, Chaejoon Cheong, Soohyun Kim

Biochem J (2009) 421 (1): 87–96.

DOI: https://doi.org/10.1042/BJ20082170

Published: 12 June 2009

... the synchrotron beamlines (4A and 6C) at the Pohang Accelerator Laboratory. Diffraction data for the structure determination were obtained using the synchrotron beamline at Spring-8, Japan, and were processed using HKL-2000 package. arylphorin ecdysone glycosylation protein stability protein structure...

View article titled, The presence of monoglucosylated N196-glycan is important for the structural stability of storage protein, arylphorin

Includes: Supplementary data

Articles

Genomic and structural aspects of protein evolution

Cyrus Chothia, Julian Gough

Biochem J (2009) 419 (1): 15–28.

DOI: https://doi.org/10.1042/BJ20090122

Published: 13 March 2009

... to combine with domains from many different superfamilies. Examination of the domain combinations described in the SUPERFAMILY database showed that there is indeed a high correlation between domain abundance and domain versatility ( r 2 =0.75) [ 63 ]. Alternative splicing can affect protein structure...

View article titled, Genomic and structural aspects of protein evolution

Articles

Caf1A usher possesses a Caf1 subunit-like domain that is crucial for Caf1 fibre secretion

Xiaodi Yu, Ganeshram R. Visweswaran, Zoe Duck, Srisailam Marupakula, Sheila MacIntyre, Stefan D. Knight, Anton V. Zavialov

Biochem J (2009) 418 (3): 541–551.

DOI: https://doi.org/10.1042/BJ20080992

Published: 25 February 2009

... region) will appear in the Protein Data Bank under accession code 3FCG. 19 5 2008 3 11 2008 25 11 2008 25 11 2008 © The Authors Journal compilation © 2009 Biochemical Society 2009 assembly chaperone/usher pathway fimbrial adhesins protein structure secretion...

View article titled, Caf1A usher possesses a Caf1 subunit-like domain that is crucial for Caf1 fibre secretion

Includes: Supplementary data

Articles

Characterization of the activity and folding of the glutathione transferase from Escherichia coli and the roles of residues Cys 10 and His 106

Xin-Yu Wang, Zai-Rong Zhang, Sarah Perrett

Biochem J (2009) 417 (1): 55–64.

DOI: https://doi.org/10.1042/BJ20071702

Published: 12 December 2008

... by addition of EGST. enzyme activity glutathione transferase (GST) protein folding protein structure GSTs (glutathione transferases; EC 2.5.1.18) are a large family of enzymes involved in cellular detoxification; they catalyse the reduction of electrophilic substrates into non-harmful...

View article titled, Characterization of the activity and folding of the glutathione transferase from Escherichia coli and the roles of residues Cys 10 and His 106

Articles

Protein glycation in vivo : functional and structural effects on yeast enolase

Ricardo A. Gomes, Luís M. A. Oliveira, Mariana Silva, Carla Ascenso, Alexandre Quintas, Gonçalo Costa, Ana V. Coelho, Marta Sousa Silva, António E. N. Ferreira, Ana Ponces Freire, Carlos Cordeiro

Biochem J (2008) 416 (3): 317–326.

DOI: https://doi.org/10.1042/BJ20080632

Published: 26 November 2008

... methylglyoxal-derived advanced glycation end-product (MAGE) protein glycation protein structure Protein glycation is a non-enzymatic post-translational modification where arginine and lysine side-chain amino groups are irreversibly modified by carbonyl compounds, forming AGEs (advanced glycation end...

View article titled, Protein glycation in vivo : functional and structural effects on yeast enolase

Articles

Structural and kinetic differences between human and Aspergillus fumigatusD-glucosamine-6-phosphate N-acetyltransferase

Ramon Hurtado-Guerrero, Olawale G. Raimi, Jinrong Min, Hong Zeng, Laura Vallius, Sharon Shepherd, Adel F. M. Ibrahim, Hong Wu, Alexander N. Plotnikov, Daan M. F. van Aalten

Biochem J (2008) 415 (2): 217–223.

DOI: https://doi.org/10.1042/BJ20081000

Published: 25 September 2008

...), and eluted with a linear gradient of NaCl up to a concentration of 500 mM (20 column volumes). The purification yield was 25 mg of the protein per 1 litre of culture. Aspergillus fumigatus inhibitor design kinetics mutagenesis protein structure UDP-GlcNAc biosynthesis X-ray crystallography...

View article titled, Structural and kinetic differences between human and Aspergillus fumigatusD-glucosamine-6-phosphate N-acetyltransferase

Articles

The guanine-nucleotide-exchange factor BopE from Burkholderia pseudomallei adopts a compact version of the Salmonella SopE/SopE2 fold and undergoes a closed-to-open conformational change upon interaction with Cdc42

Abhishek Upadhyay, Huan-Lin Wu, Christopher Williams, Terry Field, Edouard E. Galyov, Jean M. H. van den Elsen, Stefan Bagby

Biochem J (2008) 411 (3): 485–493.

DOI: https://doi.org/10.1042/BJ20071546

Published: 14 April 2008

...-nucleotide-exchange factor protein–protein interaction protein structure Rho GTPase type III secretion Cdc42Δ7 was loaded at 25 °C for 10 min with [ 3 H]GDP in a reaction buffer containing 30 mM Hepes, 100 mM KCl, 0.1 mM EDTA (pH 7.5), 1 μg of creatine phosphokinase (Sigma) and 0.5 mM DTT...

View article titled, The guanine-nucleotide-exchange factor BopE from Burkholderia pseudomallei adopts a compact version of the Salmonella SopE/SopE2 fold and undergoes a closed-to-open conformational change upon interaction with Cdc42

Includes: Supplementary data

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