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Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites
2017
Nucleic Acids Research
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M-CSA (Mechanism and Catalytic Site Atlas) is a database of enzyme active sites and reaction mechanisms that can be accessed at www.ebi.ac.uk/ thornton-srv/m-csa. ...
M-CSA results from the merging of two existing databases, MACiE (Mechanism, Annotation and Classification in Enzymes), a database of enzyme mechanisms, and CSA (Catalytic Site Atlas), a database of catalytic ...
ACKNOWLEDGEMENTS The authors would like to thank Neera Borkakoti, Roman Laskowski and John Mitchell for helpful discussions. ...
doi:10.1093/nar/gkx1012
pmid:29106569
pmcid:PMC5753290
fatcat:sep5alggufdb7msnnlsx47dlmq
A global analysis of function and conservation of catalytic residues in enzymes
2019
Journal of Biological Chemistry
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Here, we review the data on the catalytic residues of 648 enzymes, as annotated in the Mechanism and Catalytic Site Atlas (M-CSA), and compare our results with those in previous studies. ...
The catalytic residues of an enzyme comprise the amino acids located in the active center responsible for accelerating the enzyme-catalyzed reaction. ...
Enzymes (MACiE), a database of enzyme mechanisms (22, 23) , and Catalytic Site Atlas (CSA) (22, 23) , a database of catalytic sites (24, 25) . ...
doi:10.1074/jbc.rev119.006289
pmid:31796628
pmcid:PMC6956550
fatcat:umxyfl7xvzbkngv6nuwrvghboy
Graph Transformation for Enzymatic Mechanisms
[article]
2021
arXiv
pre-print
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We derive about 1000 rules for amino acid side chain chemistry from the M-CSA database, a curated repository of enzymatic mechanisms. ...
Using graph transformation we are able to propose hundreds of hypothetical catalytic mechanisms for a large number of unrelated reactions in the Rhea database. ...
Acknowledgments The authors gratefully acknowledge Leon Middelboe Hansen and Mikkel Pilegaard for providing scripts constituting the preliminary analysis of the rules. ...
arXiv:2102.03292v2
fatcat:2bpmmjmuynapbcl4ddt56b3bki
Graph transformation for enzymatic mechanisms
2021
Bioinformatics
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We derive about 1000 rules for amino acid side chain chemistry from the M-CSA database, a curated repository of enzymatic mechanisms. ...
Using graph transformation, we are able to propose hundreds of hypothetical catalytic mechanisms for a large number of unrelated reactions in the Rhea database. ...
Acknowledgements The authors gratefully acknowledge Leon Middelboe Hansen and Mikkel Pilegaard for providing scripts constituting the preliminary analysis of the rules. ...
doi:10.1093/bioinformatics/btab296
pmid:34252947
pmcid:PMC8686676
fatcat:bdnijoqtjvgunm4wlbbunib43u
Representing catalytic mechanisms with rule composition
[article]
2022
arXiv
pre-print
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In a first application, we exploit mechanistic information in the Mechanism and Catalytic Site Atlas to construct overlay graphs of hydrolase reactions listed in the database. ...
These graphs point at a spectrum of catalytic entanglement of enzyme and substrate, de-emphasizing the notion of a singular catalyst in favor of a collection of catalytic sites that can be distributed ...
Acknowledgments This work is supported by the Novo Nordisk Foundation grant NNF19OC0057834 and by the Independent Research Fund Denmark, Natural Sciences, grants DFF-0135-00420B and DFF-7014-00041. ...
arXiv:2201.04515v2
fatcat:xx5uwzh4s5cj7hezlu7daq3oga
Machine Learning Differentiates Enzymatic and Non-Enzymatic Metals in Proteins
[article]
2021
bioRxiv
pre-print
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Identifying enzyme active sites is an important task in enzymology. Metalloenzymes are 40% of all enzymes and can perform all seven classes of enzyme reactions. ...
The ability of our model to correctly identify which metal sites are responsible for enzymatic activity could assist with identifying new enzymatic mechanisms or designing de novo enzymes. ...
Acknowledgments: We gratefully acknowledge helpful conversations and manuscript edits from members of the Slusky lab as well as Yusuf Adeshina, and Adam Pogorny, We appreciate Patrick Mahomes for inspiring ...
doi:10.1101/2021.02.01.429261
fatcat:f6jfwkitejei3nnw5yamb3ncxa
EnzyMine: a comprehensive database for enzyme function annotation with enzymatic reaction chemical feature
2020
Database: The Journal of Biological Databases and Curation
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Therefore, global mining of enzymatic reactions will offer a unique landscape for researchers to understand the basic functional mechanisms of natural bioprocesses and facilitate enzyme function annotation ...
EnzyMine represents an advanced database that extends enzyme knowledge by incorporating reaction chemical feature strategies, strengthening the connectivity between enzyme and metabolic reactions. ...
A specific collection of catalytic residues and detailed processes of catalytic mechanisms can be obtained from M-CSA (7) . ...
doi:10.1093/database/baaa065
pmid:33002112
fatcat:kcbu33zg4baenj5yrcrohclxqe
Machine learning differentiates enzymatic and non-enzymatic metals in proteins
2021
Nature Communications
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AbstractMetalloenzymes are 40% of all enzymes and can perform all seven classes of enzyme reactions. ...
We anticipate that our model's ability to correctly identify which metal sites are responsible for enzymatic activity could enable identification of new enzymatic mechanisms and de novo enzyme design. ...
Acknowledgements We gratefully acknowledge helpful conversations and paper edits from members of the Slusky lab as well as Yusuf Adeshina and Adam Pogorny. ...
doi:10.1038/s41467-021-24070-3
pmid:34140507
fatcat:oy2vjdj7xfblzgseg73jvmg3ba
Capturing the geometry, function, and evolution of enzymes with 3D templates
[article]
2022
arXiv
pre-print
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Therefore, we anticipate that template-based functional site detection will be a powerful tool in the task of characterising a vast number of new protein models. ...
Structural templates are 3D signatures representing protein functional sites, such as ligand binding cavities, metal coordination motifs or catalytic sites. ...
Acknowledgements The work was supported by: the EMBL International PhD Programme (IGR) and the European Molecular Biology Laboratory (JMT) ...
arXiv:2203.02687v1
fatcat:jho4o75vuzd3xmwjmuemi2ddea
A strategy for large-scale comparison of evolutionary- and reaction-based classifications of enzyme function
2020
Database: The Journal of Biological Databases and Curation
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Historically, classification of enzyme reactions has used the enzyme nomenclature system developed to describe the overall reactions performed by biochemically characterized enzymes, irrespective of their ...
of sequences of unknown function represented in major databases. ...
helpful discussions about the design and implementation of the comparison strategy, Jeffrey Yunes for useful discussions regarding code development for generating networks and Kathy Clement for help with ...
doi:10.1093/database/baaa034
pmid:32449511
fatcat:fnfgcszyqjfttb7ulzllwir2am
Structure-Based Survey of the Human Proteome for Opportunities in Proximity Pharmacology
[article]
2022
bioRxiv
pre-print
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To survey the human proteome for opportunities in proximity pharmacology, we systematically mapped non-catalytic drug binding pockets on the structure of protein-modifying enzymes available from the Protein ...
The concept can be expanded to induce other post-translational modifications via the recruitment of different types of protein-modifying enzymes. ...
Mechanism and Catalytic Site Atlas (M-CSA): A Database of Enzyme Reaction Mechanisms and Active Sites. Nucleic Acids Res. 2018, 46 (D1), D618-D623. (16) Bateman, A.; Martin, M. ...
doi:10.1101/2022.01.13.475779
fatcat:ji2ezy2okrbdppftw74jgkgwnm
Quantifying evolutionary importance of protein sites: A Tale of two measures
2021
PLoS Genetics
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The unique requirement for the active site to selectively stabilize the transition state of the catalyzed chemical reaction imposes additional selective constraints on the rest of the enzyme. ...
Surprisingly however, catalytic sites in enzymes are the principal exception to this rule. ...
We identified catalytic sites using the Mechanism and Catalytic Site Atlas (M-CSA) [20] , ligand-binding sites using BioLip [21] , allosteric sites using the Allosteric Database (ASD) [22] [23] [24] ...
doi:10.1371/journal.pgen.1009476
pmid:33826605
fatcat:lz5exn4vnzaylnhr4pr4bjmw5m
Highlighting Human Enzymes Active in Different Metabolic Pathways and Diseases: The Case Study of EC 1.2.3.1 and EC 2.3.1.9
2020
Biomedicines
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We perform a statistics to derive our present knowledge on human metabolic pathways (the Kyoto Encyclopaedia of Genes and Genomes (KEGG)), and we found that activity aldehyde dehydrogenase (NAD(+)), described ...
sites. ...
Several databases are presently available for enzyme complete functional annotation, including BRENDA [16] , Enzyme Portal (EBI) [17] , and M-CSA (EBI) [18] . ...
doi:10.3390/biomedicines8080250
pmid:32751059
fatcat:3rk2d22brrfpveemmpkxwf4duq
A roadmap for metagenomic enzyme discovery
2021
Natural product reports (Print)
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Here we review computational and experimental strategies to discover biosynthetic enzymes from metagenomes. ...
Shotgun metagenomic approaches to uncover new enzymes are underdeveloped relative to PCR- or activity-based functional metagenomics. ...
s lab has been supported by grants of the Swiss National Science Foundation (205321_184955), the NCCR Microbiomes (51NF40_180575) and the ETH domain (PHRT #521). ...
doi:10.1039/d1np00006c
pmid:34821235
pmcid:PMC8597712
fatcat:43y3eqguw5ex5ikz7ihs7r3lg4
Activation of mitochondrial TUFM ameliorates metabolic dysregulation through coordinating autophagy induction
2021
Communications Biology
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To elucidate the mechanism underlying Kaem's biological activity, the target protein was identified via combined drug affinity responsive target stability and LC–MS/MS analyses. ...
AbstractDisorders of autophagy, a key regulator of cellular homeostasis, cause a number of human diseases. ...
), and by the Brain Korea 21 Plus Project and ICONS (Institute of Convergence Science), Yonsei University. ...
doi:10.1038/s42003-020-01566-0
pmid:33398033
fatcat:fftuh5fn4fgzdmcoskta5cw7na