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Integrated relational Enzyme database

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Presentation on theme: "Integrated relational Enzyme database"— Presentation transcript:

1 Integrated relational Enzyme database
1 August 2018 IntEnz Integrated relational Enzyme database

2 Enzymes Enzymes are proteins that catalyze chemical reactions.
Very important as many processes in biological cells need enzymes.... As there are many enzymes in the world, a classification system was invented to help identify and name them... 1 August 2018 IntEnz

3 NC-IUBMB In the 1950’s the increasing amounts of known enzymes were causing confusion. No official nomenclature system for enzymes. The IUBMB created the International Commission on Enzymes in 1956 to deal with enzyme nomenclature Later replaced with the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) 1 August 2018 IntEnz

4 EC Numbers NC-IUBMB developed the Enzyme Classification number system (EC) Classification system is based on the reactions the enzymes catalyzed Classification: Classes Subclasses Sub-subclasses EC numbers (Enzyme Commission) Example EC Each enzyme is allocated a four-digit EC number, the first three digits of which define the reaction catalysed and the fourth of which is a unique identifier (serial number). Each enzyme is also assigned a systematic name that uniquely defines the reaction catalysed. 1 August 2018 IntEnz

5 EC Classification - Classes
EC 1 – Oxidoreductases; catalyze oxidation/reduction reactions. EC 2 – Transferases; transfer a functional group e.g. Methyl group. EC 3 – Hydrolases; catalyse the hydrolysis of various bonds. EC 4 – Lyases; cleave various bonds by means other than hydrolysis and oxidation EC 5 – Isomerases; catalyse changes within one molecule. EC 6 – Ligases; joining of two molecules with concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate. Six main classes into which all enzymes are classified. 1 August 2018 IntEnz

6 EC numbers lifecycle New Rejected Private Suggested Deleted Proposed
Accepted Rejected Deleted Transferred Public Private After suggesting a new enzyme to NC-IUBMB it goes into suggested phase. This is still private phase for NC-IUBMB consumption only. After the NC-IUBMB is satisfied that it is unique, it turns into proposal for public review. If there are no objections it is accepted in the classification. Sometimes, an enzyme is proven to be inexistent or exactly the same that other one, hence the deletions and transfers. Deleted and transferred EC numbers are not reused. Proposed EC numbers may be reused. 1 August 2018 IntEnz

7 IntEnz (www.ebi.ac.uk/intenz)
IntEnz is a database focussed exclusively on Enzyme Nomenclature. 1 August 2018 IntEnz

8 What's in IntEnz Official Enzyme nomenclature from NC-IUBMB
Data from ENZYME database (SIB) Cofactors Extra cross references: UniProtKB/Swiss-Prot, Prosite Extra cross references: CSA, GO Enzyme spotlights Two different views of the same data: IntEnz ENZYME IntEnz integrates data from several sources, mainly NC-IUBMB and ENZYME, which overlap in a great extent. IntEnz is currently the relational database from whichSIB's enzyme.dat is generated. More on enzyme nomenclature on next slide. The IntEnz view show all of the data. The other views are kind of filters which resemble the NC-IUBMB and ENZYME presentations. 1 August 2018 IntEnz

9 The (official) enzyme nomenclature
Classification: Classes Subclasses Sub-subclasses EC numbers (Enzyme Commission) Nomenclature Reactions (as plain text) Comments Cross references: BRENDA, EXPASY, KEGG, ERGO, PDB, CAS registry Bibliographic references Maintained by NC-IUBMB Classification according to the catalysed reaction, independently of protein structure, origin or reaction mechanism. Dictionary of enzyme names: systematic name (precise, stresses the type of reaction), accepted name (trivial, often derived from the systematic one) and synonyms. Includes obsolete and wrong names. Reactions are the basis for the classification. NC-IUBMB manages them as plain text, which allows duplications, inconsistency in compound naming... New enzymes requests must be sent to NC-IUBMB (Trinity College, Dublin). IntEnz updates monthly with changes in Dublin's classification. 1 August 2018 IntEnz

10 IntEnz Entry Classification system Accepted Name Reaction (Rhea)
Accepted NC-IUBMB name Cofactor (ChEBI) 1 August 2018 IntEnz

11 IntEnz entry continued
UniProt Links Citations 1 August 2018 IntEnz

12 Simple Search Example 1 August 2018 IntEnz

13 Simple search Search by EC number: 1.1.1.1 1.2.3.12 1.13.1.13
Search by cross-reference: Q42884 GO: Search by enzyme name: Oxalate oxidase Agarase 3/4 collagenase Hands on! EC number (don't type 'EC'!): (no problem) is deleted, points to (changed class) is transferred to (merged with ) Name: Oxalate oxidase (EC ) agarase [ambiguous] (EC , EC ) 3/4 collagenase [obsolete] (EC ) Cross-reference: accession number (not name) Q42884 is EC GO: is EC Compound name: Caffeine gives 6 results: , , , , , CoA gives too many results! Let's try advanced search... Search by compound: Caffeine CoA 1 August 2018 IntEnz

14 Advanced Search Example
1 August 2018 IntEnz

15 Advanced search Search by reaction participant: CoA CoA-SH CoASH
Coenzyme-A Search by cofactor: CoA magnesium manganese (any) magnesium manganese (both) Reactions: CoA : 251 results. CoA-SH: no results anymore (used to get one: EC ). CoASH: no results anymore (used to get two: EC and EC ). Coenzyme-A: no results (but some in simple search, due to enzyme names, even removing the dash). WE NEED RHEA! Cofactor: CoA: 2 results. magnesium manganese (any): 227 results. magnesium manganese (both): 42 results. 1 August 2018 IntEnz

16 Browsing IntEnz Browse the whole classification from the home page
1 August 2018 IntEnz

17 Browsing via Enzyme entry
Browse upwards from an enzyme entry 1 August 2018 IntEnz

18 Downloading IntEnz IntEnzXML enzyme.dat file BioPAX level 2
Individual enzymes/all of them ASCII format/XChars-enhanced format XSD available Query/format using XSLT enzyme.dat file Generated from IntEnz for SIB BioPAX level 2 A standard exchange format for biological pathway data Based in OWL (semantic web) 1 August 2018 IntEnz

19 IntEnz team and resources
Rafael Alcántara (Developer, EBI) Kristian Axelsen (Curator, SIB) Paula de Matos (Coordinator, EBI) Anne Morgat (Curator, SIB) Christoph Steinbeck (Team leader, EBI) ftp://ftp.ebi.ac.uk/pub/databases/intenz 1 August 2018 IntEnz

20 Exercises! 1 August 2018 IntEnz

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