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    Intenz: Integrated Relational Enzyme Database

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    tri sutriani
    The document discusses IntEnz, an integrated relational enzyme database maintained by EBI and SIB. It provides background on enzyme nomenclature systems developed by IUBMB, an overview of IntEnz features like searching, browsing and downloading enzyme classification data, and contact information for the IntEnz team.

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    Intenz: Integrated Relational Enzyme Database

    Uploaded by

    tri sutriani
    18 views20 pages
    The document discusses IntEnz, an integrated relational enzyme database maintained by EBI and SIB. It provides background on enzyme nomenclature systems developed by IUBMB, an overview of IntEnz features like searching, browsing and downloading enzyme classification data, and contact information for the IntEnz team.

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    13580473

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    The document discusses IntEnz, an integrated relational enzyme database maintained by EBI and SIB. It provides background on enzyme nomenclature systems developed by IUBMB, an overview of IntEnz features like searching, browsing and downloading enzyme classification data, and contact information for the IntEnz team.

    Copyright:

    © All Rights Reserved
    Download as PPT, PDF, TXT or read online from Scribd
    Download as ppt, pdf, or txt
    18 views20 pages

    Intenz: Integrated Relational Enzyme Database

    Uploaded by

    tri sutriani
    The document discusses IntEnz, an integrated relational enzyme database maintained by EBI and SIB. It provides background on enzyme nomenclature systems developed by IUBMB, an overview of IntEnz features like searching, browsing and downloading enzyme classification data, and contact information for the IntEnz team.

    Copyright:

    © All Rights Reserved
    Download as PPT, PDF, TXT or read online from Scribd
    Download as ppt, pdf, or txt
    of 20

    October 9, 2021

    IntEnz
    Integrated relational Enzyme database

    EBI is an Outstation of the European Molecular Biology Laboratory.


    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...

    2 October 9, 2021 IntEnz


    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)

    3 October 9, 2021 IntEnz


    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 1.1.1.1

    4 October 9, 2021 IntEnz


    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.
    5 October 9, 2021 IntEnz
    EC numbers lifecycle

    New

    Private Rejected
    Suggested

    Deleted
    Proposed

    Public Transferred
    Accepted

    6 October 9, 2021 IntEnz


    IntEnz (www.ebi.ac.uk/intenz)

    7 October 9, 2021 IntEnz


    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

    8 October 9, 2021 IntEnz


    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

    9 October 9, 2021 IntEnz


    IntEnz Entry Classification
    system

    Accepted
    Name

    Reaction
    (Rhea)

    Cofactor
    (ChEBI)
    10 October 9, 2021 IntEnz
    IntEnz entry continued

    UniProt Links

    Citations

    11 October 9, 2021 IntEnz


    Simple Search Example

    12 October 9, 2021 IntEnz


    Simple search
    • Search by EC number:

    1.1.1.1

    1.2.3.12

    1.13.1.13
    • Search by cross-reference:
    Q42884
    • Search by enzyme name:
    GO:0047948
    Oxalate oxidase
    Agarase
    3/4 collagenase • Search by compound:
    Caffeine
    CoA

    13 October 9, 2021 IntEnz


    Advanced Search Example

    14 October 9, 2021 IntEnz


    Advanced search
    • Search by reaction participant:

    CoA

    CoA-SH

    CoASH

    Coenzyme-A

    • Search by cofactor:
    CoA
    magnesium manganese (any)
    magnesium manganese (both)

    15 October 9, 2021 IntEnz


    Browsing IntEnz
    • Browse the whole classification from the home page

    16 October 9, 2021 IntEnz


    Browsing via Enzyme entry

    • Browse upwards from an enzyme entry

    17 October 9, 2021 IntEnz


    Downloading IntEnz
    • IntEnzXML
    • 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)

    18 October 9, 2021 IntEnz


    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)

    http://www.ebi.ac.uk/intenz
    ftp://ftp.ebi.ac.uk/pub/databases/intenz
    http://sourceforge.net/projects/intenz
    intenz-help@lists.sourceforge.net

    19 October 9, 2021 IntEnz


    Exercises!

    http://www.ebi.ac.uk/intenz

    20 October 9, 2021 IntEnz

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