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Articles

The C-terminal structure of the N 6 -methyladenosine deaminase YerA and its role in deamination

Qian Jia, Hui Zeng, Nan Xiao, Jing Tang, Shangfang Gao, Wei Xie

Biochem J (2025) 482 (04): BCJ20240728.

https://doi.org/10.1042/BCJ20240728

Published: 12 February 2025

... of enzymes that are capable of catalyzing the deamination of 6mA to produce hypoxanthine. Despite the significance of this type of enzymes in bacterial self-defense system and potential applications as a gene-editing tool, the substrate specificity, catalytic mechanism, and physiological function of YerA...

View article titled, The C-terminal structure of the N 6 -methyladenosine deaminase YerA and its role in deamination

Includes: Supplementary data

Articles

Mapping the substrate specificity of the Plasmodium M1 and M17 aminopeptidases

Tess R. Malcolm, Karolina W. Swiderska, Brooke K. Hayes, Chaille T. Webb, Marcin Drag, Nyssa Drinkwater, Sheena McGowan

Biochem J (2021) 478 (13): 2697–2713.

https://doi.org/10.1042/BCJ20210172

Published: 16 July 2021

... and M17 aminopeptidases are both postulated to have an essential role in the terminal stages of the hemoglobin digestion process and are validated drug targets for the design of new dual-target anti-malarial compounds. In this study, we profiled the substrate specificity fingerprints and kinetic behaviors...

View article titled, Mapping the substrate specificity of the Plasmodium M1 and M17 aminopeptidases

Includes: Supplementary data

Articles

Appropriate aglycone modification significantly expands the glycan substrate acceptability of α1,6-fucosyltransferase (FUT8)

Roushu Zhang, Qiang Yang, Bhargavi M. Boruah, Guanghui Zong, Chao Li, Digantkumar Chapla, Jeong-Yeh Yang, Kelley W. Moremen, Lai-Xi Wang

Biochem J (2021) 478 (8): 1571–1583.

https://doi.org/10.1042/BCJ20210138

Published: 21 April 2021

... a GlcNAc at the non-reducing end. We describe here a further study of the substrate specificity of FUT8 using a range of N-glycans containing different aglycones. We found that FUT8 could fucosylate most of high-mannose and complex-type N-glycans, including highly branched N-glycans from chicken ovalbumin...

View article titled, Appropriate aglycone modification significantly expands the glycan substrate acceptability of α1,6-fucosyltransferase (FUT8)

Articles

Elucidating the role of GRIM-19 as a substrate and allosteric activator of pro-apoptotic serine protease HtrA2

Raghupathi Kummari, Shubhankar Dutta, Shubhangi Patil, Snehal Pandav Mudrale, Kakoli Bose

Biochem J (2021) 478 (6): 1241–1259.

https://doi.org/10.1042/BCJ20200923

Published: 19 March 2021

... and Coomassie blue staining. binding assays GRIM-19 HtrA2 in silico modelling structural changes substrate specificity Uncontrolled cell proliferation due to the non-synchronous activity of pro and anti-apoptotic proteins results in disruption of cellular homeostasis [ 1–4 ], often leading...

View article titled, Elucidating the role of GRIM-19 as a substrate and allosteric activator of pro-apoptotic serine protease HtrA2

Includes: Supplementary data

Articles

Use of the Polo-like kinase 4 (PLK4) inhibitor centrinone to investigate intracellular signalling networks using SILAC-based phosphoproteomics

Dominic P. Byrne, Christopher J. Clarke, Philip J. Brownridge, Anton Kalyuzhnyy, Simon Perkins, Amy Campbell, David Mason, Andrew R. Jones, Patrick A. Eyers, Claire E. Eyers

Biochem J (2020) 477 (13): 2451–2475.

https://doi.org/10.1042/BCJ20200309

Published: 02 July 2020

... for this article was enabled by the participation of University of Liverpool in an all-inclusive Read & Publish pilot with Portland Press and the Biochemical Society under a transformative agreement with JISC. inhibitor phosphoproteomics PLK4 protein kinase signalling substrate specificity...

View article titled, Use of the Polo-like kinase 4 (PLK4) inhibitor centrinone to investigate intracellular signalling networks using SILAC-based phosphoproteomics

Includes: Supplementary data

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.

https://doi.org/10.1042/BCJ20190812

Published: 23 December 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 specificity transpeptidase The surface proteins were displayed...

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

Articles

Structural insights into the substrate specificity of a glycoside hydrolase family 5 lichenase from Caldicellulosiruptor sp. F32

Dong-Dong Meng, Xi Liu, Sheng Dong, Ye-Fei Wang, Xiao-Qing Ma, Haixia Zhou, Xinquan Wang, Li-Shan Yao, Yingang Feng, Fu-Li Li

Biochem J (2017) 474 (20): 3373–3389.

https://doi.org/10.1042/BCJ20170328

Published: 26 September 2017

... Å resolution, which revealed that the exit subsites of substrate-binding sites contribute to both thermostability and substrate specificity of F32EG5. The sugar chain showed a sharp bend in the complex structure, suggesting that a substrate cleft fitting to the bent sugar chains in lichenan is a common feature...

View article titled, Structural insights into the substrate specificity of a glycoside hydrolase family 5 lichenase from Caldicellulosiruptor sp. F32

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.

https://doi.org/10.1042/BCJ20170174

Published: 06 July 2017

... a combination of degradomic and substrate specificity assays, we identified candidate KLK9 substrates in two different epithelial cell lines [the non-tumorigenic human keratinocyte cells (HaCaT) and the tumorigenic tongue squamous carcinoma cells (SCC9)]. Two potential KLK9 substrates [KLK10 and midkine (MDK...

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

Includes: Supplementary data

Articles

Structure and substrate fingerprint of aminopeptidase P from Plasmodium falciparum

Nyssa Drinkwater, Komagal Kannan Sivaraman, Rebecca S. Bamert, Wioletta Rut, Khadija Mohamed, Natalie B. Vinh, Peter J. Scammells, Marcin Drag, Sheena McGowan

Biochem J (2016) 473 (19): 3189–3204.

https://doi.org/10.1042/BCJ20160550

Published: 27 September 2016

... by a panel of aminopeptidases, which work in concert according to different substrate specificities, to complete protein digestion [ 14 – 16 ]. Four metalloaminopeptidases (MAPs) have been investigated for their role in peptide turnover in Pf parasites: leucyl aminopeptidase ( Pf A-M17) [ 14 , 17 ], alanyl...

View article titled, Structure and substrate fingerprint of aminopeptidase P from Plasmodium falciparum

Includes: Supplementary data

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.

https://doi.org/10.1042/BCJ20160231

Published: 28 July 2016

... the structural features required for interaction with Hgt1p, a quantitative investigation of substrate specificity of Hgt1p was carried out. Hgt1p showed a higher affinity for reduced glutathione (GSH), whereas it transported oxidized glutathione (GSSG) and other glutathione conjugates with lower affinity...

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

Includes: Supplementary data

Articles

Co-occurrence of analogous enzymes determines evolution of a novel (βα) 8 -isomerase sub-family after non-conserved mutations in flexible loop

Ernesto A. Verduzco-Castro, Karolina Michalska, Michael Endres, Ana L. Juárez-Vazquez, Lianet Noda-García, Changsoo Chang, Christopher S. Henry, Gyorgy Babnigg, Andrzej Joachimiak, Francisco Barona-Gómez

Biochem J (2016) 473 (9): 1141–1152.

https://doi.org/10.1042/BJ20151271

Published: 26 April 2016

... horizontally acquired by certain Corynebacterium species; (ii) trpF-2 , a paralogue known to be involved in synthesizing a pyrrolopyrrole moiety and (iii) trpF-3 , a variable non-conserved orthologue of trpF-1 . We previously investigated the effect of trpF-1 upon the evolution of PriA substrate specificity...

View article titled, Co-occurrence of analogous enzymes determines evolution of a novel (βα) 8 -isomerase sub-family after non-conserved mutations in flexible loop

Includes: Supplementary data

Articles

Contributions of a unique β-clamp to substrate recognition illuminates the molecular basis of exolysis in ferulic acid esterases

Robert J. Gruninger, Chris Cote, Tim A. McAllister, D. Wade Abbott

Biochem J (2016) 473 (7): 839–849.

https://doi.org/10.1042/BJ20151153

Published: 29 March 2016

... esterase Neocallimastigomycota structure–function substrate specificity Lignocellulosic biomass, a component of the plant cell wall, is a promising renewable resource for the production of a number of value added products, including biofuels, fine chemicals, livestock feedstuffs, and as a low...

View article titled, Contributions of a unique β-clamp to substrate recognition illuminates the molecular basis of exolysis in ferulic acid esterases

Includes: Multimedia, Supplementary data

Articles

Molecular evolution of the substrate specificity of ent -kaurene synthases to adapt to gibberellin biosynthesis in land plants

Manami Shimane, Yohei Ueno, Keiko Morisaki, Shingo Oogami, Masahiro Natsume, Ken-ichiro Hayashi, Hiroshi Nozaki, Hiroshi Kawaide

Biochem J (2014) 462 (3): 539–546.

https://doi.org/10.1042/BJ20140134

Published: 22 August 2014

... respectively. 30 1 2014 25 6 2014 1 7 2014 1 7 2014 © The Authors Journal compilation © 2014 Biochemical Society 2014 We analysed the function of monofunctional diterpene cyclases in Selaginella moellendorffii . Investigation of the substrate specificity of ent -kaurene...

View article titled, Molecular evolution of the substrate specificity of ent -kaurene synthases to adapt to gibberellin biosynthesis in land plants

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.

https://doi.org/10.1042/BJ20140305

Published: 10 July 2014

... -acetylspermine and N 1 -acetylspermidine, but not spermine. The molecular bases of the different substrate specificity of these two enzymes have remained so far elusive. However, previous molecular modelling, site-directed mutagenesis and biochemical characterization studies of the SMO enzyme–substrate complex...

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

Articles

Structure of a class III engineered cephalosporin acylase: comparisons with class I acylase and implications for differences in substrate specificity and catalytic activity

Emily Golden, Rachel Paterson, Wan Jun Tie, Anandhi Anandan, Gavin Flematti, Gianluca Molla, Elena Rosini, Loredano Pollegioni, Alice Vrielink

Biochem J (2013) 451 (2): 217–226.

https://doi.org/10.1042/BJ20121715

Published: 28 March 2013

... deposited in the PDB (accession codes 4HSR and 4HST respectively). crystal structure enzyme activity protein engineering substrate specificity transition state analogue Cephalosporins are currently the most widely prescribed class of antibiotics on the market and are used to treat both...

View article titled, Structure of a class III engineered cephalosporin acylase: comparisons with class I acylase and implications for differences in substrate specificity and catalytic activity

Includes: Supplementary data

Articles

Structures of trans -2-enoyl-CoA reductases from Clostridium acetobutylicum and Treponema denticola : insights into the substrate specificity and the catalytic mechanism

Kuan Hu, Meng Zhao, Tianlong Zhang, Manwu Zha, Chen Zhong, Yu Jiang, Jianping Ding

Biochem J (2013) 449 (1): 79–89.

https://doi.org/10.1042/BJ20120871

Published: 07 December 2012

... that the hydrophobic channel is optimal in both width and length for the binding of crotonyl-CoA. These results provide molecular bases for the high substrate specificity and the catalytic mechanism of TERs. We have identified CaTER ( C. acetobutylicum TER) and determined the crystal structures of CaTER...

View article titled, Structures of trans -2-enoyl-CoA reductases from Clostridium acetobutylicum and Treponema denticola : insights into the substrate specificity and the catalytic mechanism

Includes: Supplementary data

Articles

Protease activity of MALT1: a mystery unravelled

Daniel Kirchhofer, Domagoj Vucic

Biochem J (2012) 444 (2): e3–e5.

https://doi.org/10.1042/BJ20120414

Published: 11 May 2012

... mechanism and the substrate specificity of MALT1. These intriguing findings convincingly demonstrate the importance of MALT1 dimerization for its catalytic activity and pave the way for novel therapeutic approaches that target this crucial regulator of lymphoma survival and proliferation. dimerization...

View article titled, Protease activity of MALT1: a mystery unravelled

Articles

Mechanism and specificity of the human paracaspase MALT1

Janna Hachmann, Scott J. Snipas, Bram J. van Raam, Erik M. Cancino, Emily J. Houlihan, Marcin Poreba, Paulina Kasperkiewicz, Marcin Drag, Guy S. Salvesen

Biochem J (2012) 443 (1): 287–295.

https://doi.org/10.1042/BJ20120035

Published: 14 March 2012

... substrate specificity. 1 To whom correspondence should be addressed (email [email protected] ). 4 1 2012 3 2 2012 6 2 2012 6 2 2012 © 2012 The Author(s) 2012 This is an open-access article distributed under the terms of the Creative Commons Attribution Non...

View article titled, Mechanism and specificity of the human paracaspase MALT1

Articles

Evident and latent plasticity across the rice diterpene synthase family with potential implications for the evolution of diterpenoid metabolism in the cereals

Dana Morrone, Matthew L. Hillwig, Matthew E. Mead, Luke Lowry, D. Bruce Fulton, Reuben J. Peters

Biochem J (2011) 435 (3): 589–595.

https://doi.org/10.1042/BJ20101429

Published: 13 April 2011

... Biochemical Society 2011 metabolic evolution phytoalexin substrate specificity terpene synthase terpenoid natural product Assays were performed with the purified GST (glutathione transferase)–OsKSL10 fusion protein using enzymatic coupling, as described previously [ 25 , 26 ]. Briefly, GGPP...

View article titled, Evident and latent plasticity across the rice diterpene synthase family with potential implications for the evolution of diterpenoid metabolism in the cereals

Articles

Recombinant Deg/HtrA proteases from Synechocystis sp. PCC 6803 differ in substrate specificity, biochemical characteristics and mechanism

Pitter F. Huesgen, Helder Miranda, XuanTam Lam, Manuela Perthold, Holger Schuhmann, Iwona Adamska, Christiane Funk

Biochem J (2011) 435 (3): 733–742.

https://doi.org/10.1042/BJ20102131

Published: 13 April 2011

... characterization oligomerization PDZ domain serine protease substrate specificity Synechocystis sp. PCC 6803 The comparatively self-sufficient lifestyle of photosynthetic organisms comes at a price: a high inherent risk of damage to proteins and pigments by ROS (reactive oxygen species...

View article titled, Recombinant Deg/HtrA proteases from Synechocystis sp. PCC 6803 differ in substrate specificity, biochemical characteristics and mechanism

Includes: Supplementary data

Articles

Substrate specificity of haloalkane dehalogenases

Tana Koudelakova, Eva Chovancova, Jan Brezovsky, Marta Monincova, Andrea Fortova, Jiri Jarkovsky, Jiri Damborsky

Biochem J (2011) 435 (2): 345–354.

https://doi.org/10.1042/BJ20101405

Published: 29 March 2011

...Tana Koudelakova; Eva Chovancova; Jan Brezovsky; Marta Monincova; Andrea Fortova; Jiri Jarkovsky; Jiri Damborsky An enzyme's substrate specificity is one of its most important characteristics. The quantitative comparison of broad-specificity enzymes requires the selection of a homogenous set...

View article titled, Substrate specificity of haloalkane dehalogenases

Includes: Supplementary data

Articles

Crystal structure of the catalytic core of Saccharomyces cerevesiae histone demethylase Rph1: insights into the substrate specificity and catalytic mechanism

Yuanyuan Chang, Jian Wu, Xia-Jing Tong, Jin-Qiu Zhou, Jianping Ding

Biochem J (2011) 433 (2): 295–302.

https://doi.org/10.1042/BJ20101418

Published: 22 December 2010

... together, our structural and biological data provide insights into the molecular basis of the histone demethylase activity and the substrate specificity of Rph1. 1 To whom correspondence should be addressed (email [email protected] ). The structural co-ordinates of the Rph1 catalytic core...

View article titled, Crystal structure of the catalytic core of Saccharomyces cerevesiae histone demethylase Rph1: insights into the substrate specificity and catalytic mechanism

Includes: Supplementary data

Articles

Enhancement of the latent 3-isopropylmalate dehydrogenase activity of promiscuous homoisocitrate dehydrogenase by directed evolution

Yumewo Suzuki, Kuniko Asada, Junichi Miyazaki, Takeo Tomita, Tomohisa Kuzuyama, Makoto Nishiyama

Biochem J (2010) 431 (3): 401–412.

https://doi.org/10.1042/BJ20101246

Published: 11 October 2010

... been deposited in the PDB under accession code 3AH3. 9 8 2010 23 8 2010 24 8 2010 24 8 2010 © The Authors Journal compilation © 2010 Biochemical Society 2010 directed evolution DNA shuffling leucine biosynthesis lysine biosynthesis substrate specificity...

View article titled, Enhancement of the latent 3-isopropylmalate dehydrogenase activity of promiscuous homoisocitrate dehydrogenase by directed evolution

Includes: Supplementary data

Articles

Characterization of the kaurene oxidase CYP701A3, a multifunctional cytochrome P450 from gibberellin biosynthesis

Dana Morrone, Xiaoming Chen, Robert M. Coates, Reuben J. Peters

Biochem J (2010) 431 (3): 337–347.

https://doi.org/10.1042/BJ20100597

Published: 11 October 2010

... Society 2010 cytochrome P450 gibberellin hormone metabolism mono-oxygenase catalysis substrate specificity The importance of gibberellins as endogenous plant growth regulators has resulted in intensive studies on their metabolism, which has now been almost completely elucidated [ 1...

View article titled, Characterization of the kaurene oxidase CYP701A3, a multifunctional cytochrome P450 from gibberellin biosynthesis

Includes: Supplementary data

Articles

Distribution and paralogue specificity of mammalian deSUMOylating enzymes

Nagamalleswari Kolli, Jowita Mikolajczyk, Marcin Drag, Debaditya Mukhopadhyay, Nela Moffatt, Mary Dasso, Guy Salvesen, Keith D. Wilkinson

Biochem J (2010) 430 (2): 335–344.

https://doi.org/10.1042/BJ20100504

Published: 13 August 2010

... no data on this domain, it is believed to be responsible for substrate specificity and/or localization [ 29 ]. The SENP N-terminal domains vary in primary sequence and size [ 30 ]. SENP1 and SENP2 have NLSs (nuclear localization signals) and NESs (nuclear export signals) that probably play a role...

View article titled, Distribution and paralogue specificity of mammalian deSUMOylating enzymes

Includes: Supplementary data

Articles

Structural contributions of Delta class glutathione transferase active-site residues to catalysis

Jantana Wongsantichon, Robert C. Robinson, Albert J. Ketterman

Biochem J (2010) 428 (1): 25–32.

https://doi.org/10.1042/BJ20091939

Published: 28 April 2010

... 2010 Biochemical Society 2010 crystal structure glutathione transferase (GST) structural motif structure–function relationship substrate specificity GST (glutathione transferase; EC 2.5.1.18) is eminently recognized as a detoxifying enzyme that is widely distributed in all organisms...

View article titled, Structural contributions of Delta class glutathione transferase active-site residues to catalysis

Includes: Supplementary data

Articles

Pericellular activation of hepatocyte growth factor by the transmembrane serine proteases matriptase and hepsin, but not by the membrane-associated protease uPA

Kate A. Owen, Deyi Qiu, Juliano Alves, Andrew M. Schumacher, Lynette M. Kilpatrick, Jun Li, Jennifer L. Harris, Vincent Ellis

Biochem J (2010) 426 (2): 219–228.

https://doi.org/10.1042/BJ20091448

Published: 09 February 2010

... The Authors Journal compilation © 2010 Biochemical Society 2010 hepatocyte growth factor (HGF) pericellular proteolysis plasminogen activation proteolytic processing substrate specificity type-II transmembrane serine protease (TTSP) HGF (hepatocyte growth factor), also known as scatter...

View article titled, Pericellular activation of hepatocyte growth factor by the transmembrane serine proteases matriptase and hepsin, but not by the membrane-associated protease uPA

Includes: Supplementary data

Articles

A novel variant of ferredoxin-dependent sulfite reductase having preferred substrate specificity for nitrite in the unicellular red alga Cyanidioschyzon merolae

Kohsuke Sekine, Yukiko Sakakibara, Toshiharu Hase, Naoki Sato

Biochem J (2009) 423 (1): 91–98.

https://doi.org/10.1042/BJ20090581

Published: 14 September 2009

...Kohsuke Sekine; Yukiko Sakakibara; Toshiharu Hase; Naoki Sato Plant NiR (nitrite reductase) and SiR (sulfite reductase) have common structural and functional features. Both enzymes are generally distinguished in terms of substrate specificity for nitrite and sulfite. The genome of Cyanidioschyzon...

View article titled, A novel variant of ferredoxin-dependent sulfite reductase having preferred substrate specificity for nitrite in the unicellular red alga Cyanidioschyzon merolae

Includes: Supplementary data

Articles

Molecular recognition of physiological substrate noradrenaline by the adrenaline-synthesizing enzyme PNMT and factors influencing its methyltransferase activity

Nyssa Drinkwater, Christine L. Gee, Munish Puri, Kevin R. Criscione, Michael J. McLeish, Gary L. Grunewald, Jennifer L. Martin

Biochem J (2009) 422 (3): 463–471.

https://doi.org/10.1042/BJ20090702

Published: 27 August 2009

...Nyssa Drinkwater; Christine L. Gee; Munish Puri; Kevin R. Criscione; Michael J. McLeish; Gary L. Grunewald; Jennifer L. Martin Substrate specificity is critically important for enzyme catalysis. In the adrenaline-synthesizing enzyme PNMT (phenylethanolamine N -methyltransferase), minor changes...

View article titled, Molecular recognition of physiological substrate noradrenaline by the adrenaline-synthesizing enzyme PNMT and factors influencing its methyltransferase activity

Includes: Supplementary data

Articles

Crystal structure of an inverting GH 43 1,5-α-L-arabinanase from Geobacillus stearothermophilus complexed with its substrate

Anat Alhassid, Alon Ben-David, Orly Tabachnikov, Dima Libster, Einat Naveh, Gennady Zolotnitsky, Yuval Shoham, Gil Shoham

Biochem J (2009) 422 (1): 73–82.

https://doi.org/10.1042/BJ20090180

Published: 29 July 2009

... or [email protected] ). 29 1 2009 5 6 2009 8 6 2009 8 6 2009 © The Authors Journal compilation © 2009 Biochemical Society 2009 arabinanase catalytic mechanism crystal structure enzyme–substrate complex glycoside hydrolase substrate specificity Arabinan...

View article titled, Crystal structure of an inverting GH 43 1,5-α-L-arabinanase from Geobacillus stearothermophilus complexed with its substrate

Articles

Functional characterization of LePGT1, a membrane-bound prenyltransferase involved in the geranylation of p -hydroxybenzoic acid

Kazuaki Ohara, Ayumu Muroya, Nobuhiro Fukushima, Kazufumi Yazaki

Biochem J (2009) 421 (2): 231–241.

https://doi.org/10.1042/BJ20081968

Published: 26 June 2009

... accepts many prenyl substrates of different chain lengths, LePGT1 can utilize only geranyl diphosphate as its prenyl substrate. Thus the substrate specificity was analysed using chimeric enzymes derived from LePGT1 and UBIA. In vitro and in vivo analyses of the chimeras suggested that the determinant...

View article titled, Functional characterization of LePGT1, a membrane-bound prenyltransferase involved in the geranylation of p -hydroxybenzoic acid

Includes: Supplementary data

Articles

Structural and functional characterization of SplA, an exclusively specific protease of Staphylococcus aureus

Justyna Stec-Niemczyk, Katarzyna Pustelny, Magdalena Kisielewska, Michal Bista, Kevin T. Boulware, Henning R. Stennicke, Ida B. Thogersen, Patrick S. Daugherty, Jan J. Enghild, Krzysztof Baczynski, Grzegorz M. Popowicz, Adam Dubin, Jan Potempa, Grzegorz Dubin

Biochem J (2009) 419 (3): 555–564.

https://doi.org/10.1042/BJ20081351

Published: 14 April 2009

... shares a significant sequence homology to V8 protease and epidermolytic toxins which are well documented staphylococcal virulence factors. SplA has a very narrow substrate specificity apparently imposed by the precise recognition of three amino acid residues positioned N-terminal to the hydrolysed...

View article titled, Structural and functional characterization of SplA, an exclusively specific protease of Staphylococcus aureus

Includes: Supplementary data

Articles

Substrate specificity of transthyretin: identification of natural substrates in the nervous system

Márcia A. Liz, Carolina E. Fleming, Ana F. Nunes, Maria R. Almeida, Fernando M. Mar, Youngchool Choe, Charles S. Craik, James C. Powers, Matthew Bogyo, Mónica M. Sousa

Biochem J (2009) 419 (2): 467–474.

https://doi.org/10.1042/BJ20082090

Published: 27 March 2009

... (apolipoprotein A-I) after a phenylalanine residue. In the present study, we further investigated TTR substrate specificity. By using both P-diverse libraries and a library of phosphonate inhibitors, a TTR preference for a lysine residue in P1 was determined, suggesting that TTR might have a dual specificity...

View article titled, Substrate specificity of transthyretin: identification of natural substrates in the nervous system

Articles

Thermodynamic insights into the structural basis governing the donor substrate recognition by human β1,4-galactosyltransferase 7

Franck Daligault, Sophie Rahuel-Clermont, Sandrine Gulberti, Manh-Thong Cung, Guy Branlant, Patrick Netter, Jacques Magdalou, Virginie Lattard

Biochem J (2009) 418 (3): 605–614.

https://doi.org/10.1042/BJ20081093

Published: 25 February 2009

... (GAG) isothermal titration calorimetry (ITC) kinetics substrate recognition substrate specificity Human β1,4-GalT (galactosyltransferase)7 (EC 2.4.1.133, family GT7 in CAZy database, http://www.cazy.org ) is a Golgi-resident type II membrane protein that catalyses the Mn 2+ -dependent...

View article titled, Thermodynamic insights into the structural basis governing the donor substrate recognition by human β1,4-galactosyltransferase 7

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.

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

An amino acid at position 142 in nitrilase from Rhodococcus rhodochrous ATCC 33278 determines the substrate specificity for aliphatic and aromatic nitriles

Soo-Jin Yeom, Hye-Jung Kim, Jung-Kul Lee, Dong-Eun Kim, Deok-Kun Oh

Biochem J (2008) 415 (3): 401–407.

https://doi.org/10.1042/BJ20080440

Published: 15 October 2008

... by comparing with the migration length of reference proteins. aliphatic nitrile aromatic nitrile nitrilase Rhodococcus rhodochrous substrate specificity Nitrilases are enzymes widely expressed in prokaryotes and eukaryotes that hydrolyse non-peptide carbon–nitrogen bonds [ 1...

View article titled, An amino acid at position 142 in nitrilase from Rhodococcus rhodochrous ATCC 33278 determines the substrate specificity for aliphatic and aromatic nitriles

Articles

Molecular basis of the substrate specificity and the catalytic mechanism of citramalate synthase from Leptospira interrogans

Jun Ma, Peng Zhang, Zilong Zhang, Manwu Zha, Hai Xu, Guoping Zhao, Jianping Ding

Biochem J (2008) 415 (1): 45–56.

https://doi.org/10.1042/BJ20080242

Published: 12 September 2008

... and its complexes with substrates, and kinetic and mutagenesis studies of Li CMS, which together reveal the molecular basis of the high substrate specificity and the catalytic mechanism of Li CMS. The catalytic domain consists of a TIM barrel flanked by an extended C-terminal region. It forms a homodimer...

View article titled, Molecular basis of the substrate specificity and the catalytic mechanism of citramalate synthase from Leptospira interrogans

Includes: Supplementary data

Articles

Plk3 phosphorylates topoisomerase IIα at Thr 1342 , a site that is not recognized by Plk1

Masato Iida, Masao Matsuda, Hideya Komatani

Biochem J (2008) 411 (1): 27–32.

https://doi.org/10.1042/BJ20071394

Published: 13 March 2008

... differentiate their physiological roles, we compared the substrate specificities of Plk1 and Plk3 using synthetic peptides. Among these substrate peptides, topoisomerase IIα EKT 1342 DDE-containing synthetic peptide was strongly phosphorylated by Plk3 but not by Plk1. By modulating the topoisomerase IIα peptide...

View article titled, Plk3 phosphorylates topoisomerase IIα at Thr 1342 , a site that is not recognized by Plk1

Articles

Structure-based design of small peptide inhibitors of protein kinase CK2 subunit interaction

Béatrice Laudet, Caroline Barette, Vincent Dulery, Olivier Renaudet, Pascal Dumy, Alexandra Metz, Renaud Prudent, Alexandre Deshiere, Otto Dideberg, Odile Filhol, Claude Cochet

Biochem J (2007) 408 (3): 363–373.

https://doi.org/10.1042/BJ20070825

Published: 28 November 2007

... ], but CK2β is a central component of the tetrameric CK2 complex [ 13 ], controlling CK2 substrate specificity, cellular localization and enzymatic activity. In this respect, CK2β operates as a targeting subunit and/or a docking platform affecting the accessibility to the catalytic site of binding substrates...

View article titled, Structure-based design of small peptide inhibitors of protein kinase CK2 subunit interaction

Includes: Supplementary data

Articles

Engineering the substrate and inhibitor specificities of human coagulation Factor VIIa

Katrine S. Larsen, Henrik Østergaard, Jais R. Bjelke, Ole H. Olsen, Hanne B. Rasmussen, Leif Christensen, Birthe B. Kragelund, Henning R. Stennicke

Biochem J (2007) 405 (3): 429–438.

https://doi.org/10.1042/BJ20061901

Published: 13 July 2007

... profiled the primary P4–P1 substrate specificity of FVIIa using positional scanning substrate combinatorial libraries and evaluated the role of the selective active site in defining specificity. Being a trypsin-like serine protease, FVIIa had P1 specificity exclusively towards arginine and lysine residues...

View article titled, Engineering the substrate and inhibitor specificities of human coagulation Factor VIIa

Articles

Biochemical and structural exploration of the catalytic capacity of Sulfolobus KDG aldolases

Suzanne Wolterink-van Loo, André van Eerde, Marco A. J. Siemerink, Jasper Akerboom, Bauke W. Dijkstra, John van der Oost

Biochem J (2007) 403 (3): 421–430.

https://doi.org/10.1042/BJ20061419

Published: 12 April 2007

... extent. Water-mediated interactions permit binding of substrates in multiple conformations in the spacious hydrophilic binding site, and correlate with the observed broad substrate specificity. 1 These authors contributed equally to this work. 18 9 2006 8 12 2006 18 12 2006...

View article titled, Biochemical and structural exploration of the catalytic capacity of Sulfolobus KDG aldolases

Articles

Structural dissection of the reaction mechanism of cellobiose phosphorylase

Masafumi Hidaka, Motomitsu Kitaoka, Kiyoshi Hayashi, Takayoshi Wakagi, Hirofumi Shoun, Shinya Fushinobu

Biochem J (2006) 398 (1): 37–43.

https://doi.org/10.1042/BJ20060274

Published: 27 July 2006

... of the anomeric configuration. The substrate specificity and reaction mechanism of cellobiose phosphorylase from Cellvibrio gilvus have been investigated in detail. We have determined the crystal structure of the glucose-sulphate and glucose-phosphate complexes of this enzyme at a maximal resolution of 2.0 Å (1...

View article titled, Structural dissection of the reaction mechanism of cellobiose phosphorylase

Articles

Probing the substrate specificity of the dengue virus type 2 NS3 serine protease by using internally quenched fluorescent peptides

Pornwaratt Niyomrattanakit, Sviatlana Yahorava, Ilze Mutule, Felikss Mutulis, Ramona Petrovska, Peteris Prusis, Gerd Katzenmeier, Jarl E. S. Wikberg

Biochem J (2006) 397 (1): 203–211.

https://doi.org/10.1042/BJ20051767

Published: 14 June 2006

... an attractive target for the development of antiviral drugs directed at the inhibition of polyprotein processing. In the present study, we have investigated determinants of substrate specificity of the dengue virus NS3 protease by using internally quenched fluorogenic peptides containing Abz ( o -aminobenzoic...

View article titled, Probing the substrate specificity of the dengue virus type 2 NS3 serine protease by using internally quenched fluorescent peptides

Articles

Characterization of yeast pyruvate kinase 1 as a protein kinase A substrate, and specificity of the phosphorylation site sequence in the whole protein

Paula Portela, Silvia Moreno, Silvia Rossi

Biochem J (2006) 396 (1): 117–126.

https://doi.org/10.1042/BJ20051642

Published: 26 April 2006

..., the S22 peptide, indicating that ground-state substrate binding is not the major determinant of substrate specificity for PKA. 1 To whom correpsondence should be addressed (email [email protected] ). 8 10 2005 10 1 2006 20 1 2006 20 1 2006 The Biochemical Society...

View article titled, Characterization of yeast pyruvate kinase 1 as a protein kinase A substrate, and specificity of the phosphorylation site sequence in the whole protein

Articles

Hepatocyte growth factor is a preferred in vitro substrate for human hepsin, a membrane-anchored serine protease implicated in prostate and ovarian cancers

Sylvia Herter, Derek E. Piper, Wade Aaron, Timothy Gabriele, Gene Cutler, Ping Cao, Ami S. Bhatt, Youngchool Choe, Charles S. Craik, Nigel Walker, David Meininger, Timothy Hoey, Richard J. Austin

Biochem J (2005) 390 (1): 125–136.

https://doi.org/10.1042/BJ20041955

Published: 09 August 2005

... liver and tumours of the prostate and ovaries. To better understand the biological functions of hepsin, we identified macromolecular substrates employing a tetrapeptide PS-SCL (positional scanning-synthetic combinatorial library) screen that rapidly determines the P1–P4 substrate specificity. Hepsin...

View article titled, Hepatocyte growth factor is a preferred in vitro substrate for human hepsin, a membrane-anchored serine protease implicated in prostate and ovarian cancers

Includes: Supplementary data

Articles

Flexibility in substrate recognition by thimet oligopeptidase as revealed by denaturation studies

Jeffrey A. SIGMAN, Tasneem H. PATWA, Ana V. TABLANTE, Calleen D. JOSEPH, Marc J. GLUCKSMAN, Adele J. WOLFSON

Biochem J (2005) 388 (1): 255–261.

https://doi.org/10.1042/BJ20041481

Published: 10 May 2005

... TOP to recognize peptides of variable sequence [ 3 , 14 ]. denaturation metalloendopeptidase protein folding substrate specificity thimet oligopeptidase urea Thimet oligopeptidase (TOP) (EC 3.4.24.15; EP24.15) is a 78-kDa Zn(II)-dependent endopeptidase [ 1 ]. It is related to several...

View article titled, Flexibility in substrate recognition by thimet oligopeptidase as revealed by denaturation studies

Articles

Regulation of activity in vitro and in vivo of three phospholipases B from Saccharomyces cerevisiae

Olaf MERKEL, Olga V. OSKOLKOVA, Florian RAAB, Rosemarie EL-TOUKHY, Fritz PALTAUF

Biochem J (2005) 387 (2): 489–496.

https://doi.org/10.1042/BJ20041272

Published: 05 April 2005

... phospholipase B Saccharomyces cerevisiae substrate specificity Table 2 Effects of bivalent and tervalent cations on phospholipase B activity The rate of phospholipid hydrolysis was measured at set molar fractions (0.15) of phospholipid (PtdCho for Plb1p, PtdEtn for Plb2p and PtdIns for Plb3p...

View article titled, Regulation of activity in vitro and in vivo of three phospholipases B from Saccharomyces cerevisiae

Articles

Substrate and product specificities of cis -type undecaprenyl pyrophosphate synthase

Annie P.-C. CHEN, Sing-Yang CHANG, Yu-Chung LIN, Yang-Sheng SUN, Chao-Tsen CHEN, Andrew H.-J. WANG, Po-Huang LIANG

Biochem J (2005) 386 (1): 169–176.

https://doi.org/10.1042/BJ20040785

Published: 08 February 2005

...) but similar k cat value (1.7±0.1 s −1 ) compared with FPP. Replacement of L85, L88 or F89 with Ala increases FPP and GGPP K m values by the same amount, indicating that these amino acids are important for substrate binding, but do not determine substrate specificity. With GGPP as a substrate, UPPS still...

View article titled, Substrate and product specificities of cis -type undecaprenyl pyrophosphate synthase

Articles

In vitro elucidation of substrate specificity and bioassay of proprotein convertase 4 using intramolecularly quenched fluorogenic peptides

Sarmistha BASAK, Michel CHRÉTIEN, Majambu MBIKAY, Ajoy BASAK

Biochem J (2004) 380 (2): 505–514.

https://doi.org/10.1042/bj20031405

Published: 01 June 2004

.... To provide further evidence in support of this notion and also to study the substrate specificity and bioassay of PC4, a series of intramolecularly quenched fluorogenic peptides containing the cleavage sites and several mutants were prepared. A comparative kinetic analysis and measurement of V max (app)/ K m...

View article titled, In vitro elucidation of substrate specificity and bioassay of proprotein convertase 4 using intramolecularly quenched fluorogenic peptides

Articles

Catalytic- and ecto-domains of membrane type 1-matrix metalloproteinase have similar inhibition profiles but distinct endopeptidase activities

Douglas R. HURST, Martin A. SCHWARTZ, Mohammad A. GHAFFARI, Yonghao JIN, Harald TSCHESCHE, Gregg B. FIELDS, Qing-Xiang Amy SANG

Biochem J (2004) 377 (3): 775–779.

https://doi.org/10.1042/bj20031067

Published: 01 February 2004

... the structure–function relationship between the human MT1-MMP active site and the influence of the haemopexin domain on catalysis, substrate specificity and inhibition kinetics of the cdMT1-MMP (catalytic domain of MT1-MMP) and the ecto domain ΔTM-MT1-MMP (transmembrane-domain-deleted MT1-MMP) were compared...

View article titled, Catalytic- and ecto-domains of membrane type 1-matrix metalloproteinase have similar inhibition profiles but distinct endopeptidase activities

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