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Protein

GTP cyclohydrolase-2

Gene

ribA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate (DARP), formate and pyrophosphate.1 Publication

Catalytic activityi

GTP + 3 H2O = formate + 2,5-diamino-6-hydroxy-4-(5-phospho-D-ribosylamino)pyrimidine + diphosphate.

Cofactori

Zn2+2 PublicationsNote: Binds 1 zinc ion per subunit.2 Publications

Enzyme regulationi

Competitively inhibited by pyrophosphate.2 Publications

Kineticsi

  1. KM=41 µM for GTP1 Publication

    pH dependencei

    Optimum pH is 8.5.1 Publication

    Pathwayi: riboflavin biosynthesis

    This protein is involved in step 1 of the subpathway that synthesizes 5-amino-6-(D-ribitylamino)uracil from GTP.
    Proteins known to be involved in the 4 steps of the subpathway in this organism are:
    1. GTP cyclohydrolase-2 (ribA)
    2. Riboflavin biosynthesis protein RibD (ribD)
    3. Riboflavin biosynthesis protein RibD (ribD)
    4. 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YbjI (ybjI), 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigB (yigB)
    This subpathway is part of the pathway riboflavin biosynthesis, which is itself part of Cofactor biosynthesis.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes 5-amino-6-(D-ribitylamino)uracil from GTP, the pathway riboflavin biosynthesis and in Cofactor biosynthesis.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Metal bindingi54Zinc; catalytic1
    Metal bindingi65Zinc; catalytic1
    Metal bindingi67Zinc; catalytic1
    Binding sitei70GTP1
    Binding sitei114GTP1
    Active sitei126Proton acceptorSequence analysis1
    Active sitei128Nucleophile1
    Binding sitei149GTP1
    Binding sitei154GTP1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi49 – 53GTP5
    Nucleotide bindingi92 – 94GTP3

    GO - Molecular functioni

    • GTP binding Source: UniProtKB-KW
    • GTP cyclohydrolase II activity Source: EcoCyc
    • zinc ion binding Source: UniProtKB-HAMAP

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Riboflavin biosynthesis

    Keywords - Ligandi

    GTP-binding, Metal-binding, Nucleotide-binding, Zinc

    Enzyme and pathway databases

    BioCyciEcoCyc:GTP-CYCLOHYDRO-II-MONOMER.
    ECOL316407:JW1269-MONOMER.
    MetaCyc:GTP-CYCLOHYDRO-II-MONOMER.
    UniPathwayiUPA00275; UER00400.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    GTP cyclohydrolase-2 (EC:3.5.4.25)
    Alternative name(s):
    GTP cyclohydrolase II
    Gene namesi
    Name:ribA
    Ordered Locus Names:b1277, JW1269
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG11331. ribA.

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi54C → S: Loss of zinc binding. Loss of ring-opening activity. Can still remove phosphate from GTP. 1 Publication1
    Mutagenesisi65C → S: Loss of zinc binding. Loss of ring-opening activity. Can still remove phosphate from GTP. 1 Publication1
    Mutagenesisi67C → S: Loss of zinc binding. Loss of ring-opening activity. Can still remove phosphate from GTP. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001517541 – 196GTP cyclohydrolase-2Add BLAST196

    Proteomic databases

    EPDiP0A7I7.
    PaxDbiP0A7I7.
    PRIDEiP0A7I7.

    Interactioni

    Subunit structurei

    Homodimer.2 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    pyrFP082442EBI-1123314,EBI-1123202

    Protein-protein interaction databases

    DIPiDIP-36049N.
    IntActiP0A7I7. 2 interactors.
    STRINGi511145.b1277.

    Structurei

    Secondary structure

    1196
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi3 – 13Combined sources11
    Beta strandi16 – 25Combined sources10
    Turni26 – 28Combined sources3
    Beta strandi31 – 38Combined sources8
    Beta strandi42 – 44Combined sources3
    Beta strandi46 – 52Combined sources7
    Helixi55 – 58Combined sources4
    Beta strandi63 – 66Combined sources4
    Helixi67 – 81Combined sources15
    Beta strandi83 – 89Combined sources7
    Helixi92 – 95Combined sources4
    Helixi98 – 109Combined sources12
    Helixi114 – 120Combined sources7
    Helixi131 – 139Combined sources9
    Beta strandi144 – 148Combined sources5
    Helixi152 – 160Combined sources9
    Beta strandi165 – 169Combined sources5

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2BZ0X-ray2.60A/B1-196[»]
    2BZ1X-ray1.54A1-196[»]
    ProteinModelPortaliP0A7I7.
    SMRiP0A7I7.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0A7I7.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the GTP cyclohydrolase II family.Curated

    Phylogenomic databases

    eggNOGiENOG4107T1C. Bacteria.
    COG0807. LUCA.
    HOGENOMiHOG000115442.
    InParanoidiP0A7I7.
    KOiK01497.
    OMAiPTPFGVF.
    PhylomeDBiP0A7I7.

    Family and domain databases

    CDDicd00641. GTP_cyclohydro2. 1 hit.
    HAMAPiMF_00179. RibA. 1 hit.
    InterProiIPR032677. GTP_cyclohydro_II.
    IPR000926. RibA.
    [Graphical view]
    PfamiPF00925. GTP_cyclohydro2. 1 hit.
    [Graphical view]
    SUPFAMiSSF142695. SSF142695. 1 hit.
    TIGRFAMsiTIGR00505. ribA. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P0A7I7-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MQLKRVAEAK LPTPWGDFLM VGFEELATGH DHVALVYGDI SGHTPVLARV
    60 70 80 90 100
    HSECLTGDAL FSLRCDCGFQ LEAALTQIAE EGRGILLYHR QEGRNIGLLN
    110 120 130 140 150
    KIRAYALQDQ GYDTVEANHQ LGFAADERDF TLCADMFKLL GVNEVRLLTN
    160 170 180 190
    NPKKVEILTE AGINIVERVP LIVGRNPNNE HYLDTKAEKM GHLLNK
    Length:196
    Mass (Da):21,836
    Last modified:June 7, 2005 - v1
    Checksum:iC22FED98F48098DF
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X67876 Genomic DNA. Translation: CAA48075.1.
    U00096 Genomic DNA. Translation: AAC74359.1.
    AP009048 Genomic DNA. Translation: BAA14831.1.
    X60293 Genomic DNA. Translation: CAA42835.1.
    PIRiA40654.
    RefSeqiNP_415793.1. NC_000913.3.
    WP_001176295.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC74359; AAC74359; b1277.
    BAA14831; BAA14831; BAA14831.
    GeneIDi945763.
    KEGGiecj:JW1269.
    eco:b1277.
    PATRICi32117816. VBIEscCol129921_1328.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X67876 Genomic DNA. Translation: CAA48075.1.
    U00096 Genomic DNA. Translation: AAC74359.1.
    AP009048 Genomic DNA. Translation: BAA14831.1.
    X60293 Genomic DNA. Translation: CAA42835.1.
    PIRiA40654.
    RefSeqiNP_415793.1. NC_000913.3.
    WP_001176295.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2BZ0X-ray2.60A/B1-196[»]
    2BZ1X-ray1.54A1-196[»]
    ProteinModelPortaliP0A7I7.
    SMRiP0A7I7.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    DIPiDIP-36049N.
    IntActiP0A7I7. 2 interactors.
    STRINGi511145.b1277.

    Proteomic databases

    EPDiP0A7I7.
    PaxDbiP0A7I7.
    PRIDEiP0A7I7.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC74359; AAC74359; b1277.
    BAA14831; BAA14831; BAA14831.
    GeneIDi945763.
    KEGGiecj:JW1269.
    eco:b1277.
    PATRICi32117816. VBIEscCol129921_1328.

    Organism-specific databases

    EchoBASEiEB1307.
    EcoGeneiEG11331. ribA.

    Phylogenomic databases

    eggNOGiENOG4107T1C. Bacteria.
    COG0807. LUCA.
    HOGENOMiHOG000115442.
    InParanoidiP0A7I7.
    KOiK01497.
    OMAiPTPFGVF.
    PhylomeDBiP0A7I7.

    Enzyme and pathway databases

    UniPathwayiUPA00275; UER00400.
    BioCyciEcoCyc:GTP-CYCLOHYDRO-II-MONOMER.
    ECOL316407:JW1269-MONOMER.
    MetaCyc:GTP-CYCLOHYDRO-II-MONOMER.

    Miscellaneous databases

    EvolutionaryTraceiP0A7I7.
    PROiP0A7I7.

    Family and domain databases

    CDDicd00641. GTP_cyclohydro2. 1 hit.
    HAMAPiMF_00179. RibA. 1 hit.
    InterProiIPR032677. GTP_cyclohydro_II.
    IPR000926. RibA.
    [Graphical view]
    PfamiPF00925. GTP_cyclohydro2. 1 hit.
    [Graphical view]
    SUPFAMiSSF142695. SSF142695. 1 hit.
    TIGRFAMsiTIGR00505. ribA. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiRIBA_ECOLI
    AccessioniPrimary (citable) accession number: P0A7I7
    Secondary accession number(s): P25523, P78147
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 7, 2005
    Last sequence update: June 7, 2005
    Last modified: November 2, 2016
    This is version 92 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Catalyzes the formation of GMP as minor product, with concomitant release of pyrophosphate. Release of pyrophosphate requires magnesium ions.

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.