R3CW39 last accessed: 2022-11-04

Other names: M-CSA, CSA (formerly), Catalytic Site Atlas (formerly)

M-CSA is a database of enzyme reaction mechanisms. It provides annotation on the protein, catalytic residues, cofactors, and the reaction mechanisms of hundreds of enzymes. There are two kinds of entries in M-CSA: 'Detailed mechanism' entries are more complete and show the individual chemical steps of the mechanism as schemes with electron flow arrows; and 'Catalytic Site' entries annotate the catalytic residues necessary for the reaction, but do not show the mechanism.

Webpage:

https://www.ebi.ac.uk/thornton-srv/m-csa/

Licence:

Name: Creative Commons Attribution-NoDerivs 3.0 Unported (CC BY-ND 3.0)
URL: https://creativecommons.org/licenses/by-nd/3.0/

Publications:

Publications
More detailed information about this field from each metasource.

Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites
PMID: 29106569
metasource: Fairsharing.org
version: FAIRsharing.org: M-CSA; Mechanism and Catalytic Site Atlas; DOI: https://doi.org/10.25504/FAIRsharing.BrubDI; Last edited: May 4, 2020, 11:08 a.m.; Last accessed: Jan 03 2022 7:06 p.m.

http://dx.doi.org/10.1093/nar/gkx1012
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites PubMed citations: 42.

42 articles citing: Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites

Menthol carbonates as potent antiparasitic agents: synthesis and in vitro studies along with computer-aided approaches. PMID:35698116
Electrostatic fingerprints of catalytically active amino acids in enzymes. PMID:35481659
3DLigandSite: structure-based prediction of protein-ligand binding sites. PMID:35412635
Protein cost minimization promotes the emergence of coenzyme redundancy. PMID:35344442
Conformational Variation in Enzyme Catalysis: A Structural Study on Catalytic Residues. PMID:35240125
Florigen and its homologs of FT/CETS/PEBP/RKIP/YbhB family may be the enzymes of small molecule metabolism: review of the evidence. PMID:35086479
Worldwide Protein Data Bank (wwPDB): A virtual treasure for research in biotechnology. PMID:34908533
A roadmap for metagenomic enzyme discovery. PMID:34821235
Rhea, the reaction knowledgebase in 2022. PMID:34755880
PDBe-KB: collaboratively defining the biological context of structural data. PMID:34755867
Machine learning for enzyme engineering, selection and design. PMID:34296736
Graph transformation for enzymatic mechanisms. PMID:34252947
Machine learning differentiates enzymatic and non-enzymatic metals in proteins. PMID:34140507
BENZ WS: the Bologna ENZyme Web Server for four-level EC number annotation. PMID:33963861
Quantifying evolutionary importance of protein sites: A Tale of two measures. PMID:33826605
Addressing uncertainty in genome-scale metabolic model reconstruction and analysis. PMID:33602294
Water and Life: The Medium is the Message. PMID:33427903
An automated protocol for modelling peptide substrates to proteases. PMID:33375946
The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies. PMID:33348379
FireProtASR: A Web Server for Fully Automated Ancestral Sequence Reconstruction. PMID:33346815
Real-time structural motif searching in proteins using an inverted index strategy. PMID:33284792
CATH functional families predict functional sites in proteins. PMID:33135053
A strategy for large-scale comparison of evolutionary- and reaction-based classifications of enzyme function. PMID:32449511
The Hitchhiker's guide to biocatalysis: recent advances in the use of enzymes in organic synthesis. PMID:32206264
Developing and applying computational resources for biochemistry education. PMID:32203640
Autocatalytic chemical networks at the origin of metabolism. PMID:32156207
A Benchmark for Homomeric Enzyme Active Site Structure Prediction Highlights the Importance of Accurate Modeling of Protein Symmetry. PMID:31909318
A global analysis of function and conservation of catalytic residues in enzymes. PMID:31796628
Environmental boundary conditions for the origin of life converge to an organo-sulfur metabolism. PMID:31712697
MANET 3.0: Hierarchy and modularity in evolving metabolic networks. PMID:31648227
Challenges in the annotation of pseudoenzymes in databases: the UniProtKB approach. PMID:31618524
PDBe-KB: a community-driven resource for structural and functional annotations. PMID:31584092
funtrp: identifying protein positions for variation driven functional tuning. PMID:31584091
VarMap: a web tool for mapping genomic coordinates to protein sequence and structure and retrieving protein structural annotations. PMID:31192369
Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport. PMID:31114897
Characterization of recombinant endo-1,4-β-xylanase of Bacillus halodurans C-125 and rational identification of hot spot amino acid residues responsible for enhancing thermostability by an in-silico approach. PMID:31079316
PIRSitePredict for protein functional site prediction using position-specific rules. PMID:30805646
CATH: expanding the horizons of structure-based functional annotations for genome sequences. PMID:30398663
Updates in Rhea: SPARQLing biochemical reaction data. PMID:30272209
Ranking Enzyme Structures in the PDB by Bound Ligand Similarity to Biological Substrates. PMID:29551288
The 2018 Nucleic Acids Research database issue and the online molecular biology database collection. PMID:29316735
The European Bioinformatics Institute in 2017: data coordination and integration. PMID:29186510
http://dx.doi.org/10.1093/nar/gkx1012

Tags:

Tags
More detailed information about this field from each metasource.

annotation
metasource: Fairsharing.org
version: FAIRsharing.org: M-CSA; Mechanism and Catalytic Site Atlas; DOI: https://doi.org/10.25504/FAIRsharing.BrubDI; Last edited: May 4, 2020, 11:08 a.m.; Last accessed: Jan 03 2022 7:06 p.m.

catalytic activity
metasource: Fairsharing.org
version: FAIRsharing.org: M-CSA; Mechanism and Catalytic Site Atlas; DOI: https://doi.org/10.25504/FAIRsharing.BrubDI; Last edited: May 4, 2020, 11:08 a.m.; Last accessed: Jan 03 2022 7:06 p.m.

enzymatic reaction
metasource: Fairsharing.org
version: FAIRsharing.org: M-CSA; Mechanism and Catalytic Site Atlas; DOI: https://doi.org/10.25504/FAIRsharing.BrubDI; Last edited: May 4, 2020, 11:08 a.m.; Last accessed: Jan 03 2022 7:06 p.m.

enzyme
metasource: Fairsharing.org
version: FAIRsharing.org: M-CSA; Mechanism and Catalytic Site Atlas; DOI: https://doi.org/10.25504/FAIRsharing.BrubDI; Last edited: May 4, 2020, 11:08 a.m.; Last accessed: Jan 03 2022 7:06 p.m.

metabolic and signaling pathways
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

enzymes and enzyme nomenclature
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

3d structure
metasource: re3data.org
version: re3data.org: Mechanism and Catalytic Site Atlas; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CW39 last accessed: 2022-11-04

activation (chemistry)
metasource: re3data.org
version: re3data.org: Mechanism and Catalytic Site Atlas; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CW39 last accessed: 2022-11-04

amino acids
metasource: re3data.org
version: re3data.org: Mechanism and Catalytic Site Atlas; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CW39 last accessed: 2022-11-04

catalysis
metasource: re3data.org
version: re3data.org: Mechanism and Catalytic Site Atlas; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CW39 last accessed: 2022-11-04

enzymes
metasource: re3data.org
version: re3data.org: Mechanism and Catalytic Site Atlas; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CW39 last accessed: 2022-11-04

proteins
metasource: re3data.org
version: re3data.org: Mechanism and Catalytic Site Atlas; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CW39 last accessed: 2022-11-04

catalytic activity enzymatic reaction enzyme metabolic and signaling pathways enzymes and enzyme nomenclature 3d structure activation (chemistry) amino acids catalysis enzyme proteins

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