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Q5SKW7

- GCSPB_THET8

UniProt

Q5SKW7 - GCSPB_THET8

Protein

Probable glycine dehydrogenase (decarboxylating) subunit 2

Gene

gcvPB

Organism
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 68 (01 Oct 2014)
      Sequence version 1 (21 Dec 2004)
      Previous versions | rss
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    Functioni

    The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO2 is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein.UniRule annotation

    Catalytic activityi

    Glycine + [glycine-cleavage complex H protein]-N(6)-lipoyl-L-lysine = [glycine-cleavage complex H protein]-S-aminomethyl-N(6)-dihydrolipoyl-L-lysine + CO2.UniRule annotation

    Cofactori

    Pyridoxal phosphate.UniRule annotation

    GO - Molecular functioni

    1. glycine dehydrogenase (decarboxylating) activity Source: UniProtKB-EC
    2. pyridoxal phosphate binding Source: InterPro

    GO - Biological processi

    1. glycine decarboxylation via glycine cleavage system Source: UniProtKB-HAMAP

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Ligandi

    Pyridoxal phosphate

    Enzyme and pathway databases

    BioCyciTTHE300852:GH8R-551-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Probable glycine dehydrogenase (decarboxylating) subunit 2UniRule annotation (EC:1.4.4.2UniRule annotation)
    Alternative name(s):
    Glycine cleavage system P-protein subunit 2UniRule annotation
    Glycine decarboxylase subunit 2UniRule annotation
    Glycine dehydrogenase (aminomethyl-transferring) subunit 2UniRule annotation
    Gene namesi
    Name:gcvPBUniRule annotation
    Ordered Locus Names:TTHA0526
    OrganismiThermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
    Taxonomic identifieri300852 [NCBI]
    Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus
    ProteomesiUP000000532: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 474474Probable glycine dehydrogenase (decarboxylating) subunit 2PRO_1000045709Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei266 – 2661N6-(pyridoxal phosphate)lysineUniRule annotation

    Interactioni

    Subunit structurei

    The glycine cleavage system is composed of four proteins: P, T, L and H. In this organism, the P 'protein' is a heterodimer of two subunits.UniRule annotation

    Protein-protein interaction databases

    STRINGi300852.TTHA0526.

    Structurei

    Secondary structure

    1
    474
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi6 – 94
    Helixi26 – 294
    Helixi32 – 343
    Helixi47 – 5812
    Turni64 – 663
    Turni72 – 743
    Helixi81 – 888
    Helixi99 – 1013
    Helixi103 – 12018
    Beta strandi123 – 1264
    Helixi132 – 14918
    Turni153 – 1553
    Beta strandi158 – 1625
    Helixi168 – 1758
    Beta strandi179 – 1835
    Beta strandi189 – 1913
    Helixi193 – 1997
    Beta strandi204 – 2096
    Helixi222 – 23110
    Beta strandi235 – 2395
    Helixi240 – 2456
    Turni246 – 2494
    Helixi252 – 2554
    Beta strandi258 – 2614
    Turni264 – 2685
    Helixi273 – 2753
    Beta strandi282 – 2843
    Helixi286 – 2916
    Beta strandi296 – 2994
    Beta strandi304 – 3074
    Beta strandi317 – 3193
    Helixi324 – 36239
    Beta strandi377 – 3804
    Helixi387 – 39610
    Beta strandi403 – 4053
    Beta strandi414 – 4163
    Helixi424 – 43815
    Helixi442 – 4465
    Beta strandi451 – 4544
    Helixi459 – 4646
    Beta strandi469 – 4713

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1WYTX-ray2.40B/D1-474[»]
    1WYUX-ray2.10B/D/F/H1-474[»]
    1WYVX-ray2.40B/D/F/H1-474[»]
    ProteinModelPortaliQ5SKW7.
    SMRiQ5SKW7. Positions 2-474.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ5SKW7.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the GcvP family. C-terminal subunit subfamily.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG1003.
    HOGENOMiHOG000239368.
    KOiK00283.
    OMAiWTGLMMI.
    OrthoDBiEOG6HMXDX.
    PhylomeDBiQ5SKW7.

    Family and domain databases

    Gene3Di3.40.640.10. 1 hit.
    HAMAPiMF_00713. GcvPB.
    InterProiIPR020580. GDC-P_N.
    IPR020581. GDC_P.
    IPR023012. GDC_P_su2.
    IPR015424. PyrdxlP-dep_Trfase.
    IPR015421. PyrdxlP-dep_Trfase_major_sub1.
    [Graphical view]
    PANTHERiPTHR11773. PTHR11773. 1 hit.
    PfamiPF02347. GDC-P. 1 hit.
    [Graphical view]
    SUPFAMiSSF53383. SSF53383. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q5SKW7-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSFPLIFERS RKGRRGLKLV KAVPKAEDLI PKEHLREVPP RLPEVDELTL    50
    VRHYTGLSRR QVGVDTTFYP LGSCTMKYNP KLHEEAARLF ADLHPYQDPR 100
    TAQGALRLMW ELGEYLKALT GMDAITLEPA AGAHGELTGI LIIRAYHEDR 150
    GEGRTRRVVL VPDSAHGSNP ATASMAGYQV REIPSGPEGE VDLEALKREL 200
    GPHVAALMLT NPNTLGLFER RILEISRLCK EAGVQLYYDG ANLNAIMGWA 250
    RPGDMGFDVV HLNLHKTFTV PHGGGGPGSG PVGVKAHLAP YLPVPLVERG 300
    EEGFYLDFDR PKSIGRVRSF YGNFLALVRA WAYIRTLGLE GLKKAAALAV 350
    LNARYLKELL KEKGYRVPYD GPSMHEFVAQ PPEGFRALDL AKGLLELGFH 400
    PPTVYFPLIV KEALMVEPTE TEAKETLEAF AEAMGALLKK PKEWLENAPY 450
    STPVRRLDEL RANKHPKLTY FDEG 474
    Length:474
    Mass (Da):52,709
    Last modified:December 21, 2004 - v1
    Checksum:iA8B48175AF156C1D
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AP008226 Genomic DNA. Translation: BAD70349.1.
    RefSeqiWP_011228003.1. NC_006461.1.
    YP_143792.1. NC_006461.1.

    Genome annotation databases

    EnsemblBacteriaiBAD70349; BAD70349; BAD70349.
    GeneIDi3168946.
    KEGGittj:TTHA0526.
    PATRICi23956027. VBITheThe93045_0524.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AP008226 Genomic DNA. Translation: BAD70349.1 .
    RefSeqi WP_011228003.1. NC_006461.1.
    YP_143792.1. NC_006461.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1WYT X-ray 2.40 B/D 1-474 [» ]
    1WYU X-ray 2.10 B/D/F/H 1-474 [» ]
    1WYV X-ray 2.40 B/D/F/H 1-474 [» ]
    ProteinModelPortali Q5SKW7.
    SMRi Q5SKW7. Positions 2-474.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 300852.TTHA0526.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai BAD70349 ; BAD70349 ; BAD70349 .
    GeneIDi 3168946.
    KEGGi ttj:TTHA0526.
    PATRICi 23956027. VBITheThe93045_0524.

    Phylogenomic databases

    eggNOGi COG1003.
    HOGENOMi HOG000239368.
    KOi K00283.
    OMAi WTGLMMI.
    OrthoDBi EOG6HMXDX.
    PhylomeDBi Q5SKW7.

    Enzyme and pathway databases

    BioCyci TTHE300852:GH8R-551-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei Q5SKW7.

    Family and domain databases

    Gene3Di 3.40.640.10. 1 hit.
    HAMAPi MF_00713. GcvPB.
    InterProi IPR020580. GDC-P_N.
    IPR020581. GDC_P.
    IPR023012. GDC_P_su2.
    IPR015424. PyrdxlP-dep_Trfase.
    IPR015421. PyrdxlP-dep_Trfase_major_sub1.
    [Graphical view ]
    PANTHERi PTHR11773. PTHR11773. 1 hit.
    Pfami PF02347. GDC-P. 1 hit.
    [Graphical view ]
    SUPFAMi SSF53383. SSF53383. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Complete genome sequence of Thermus thermophilus HB8."
      Masui R., Kurokawa K., Nakagawa N., Tokunaga F., Koyama Y., Shibata T., Oshima T., Yokoyama S., Yasunaga T., Kuramitsu S.
      Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: HB8 / ATCC 27634 / DSM 579.
    2. "Structure of P-protein of the glycine cleavage system: implications for nonketotic hyperglycinemia."
      Nakai T., Nakagawa N., Maoka N., Masui R., Kuramitsu S., Kamiya N.
      EMBO J. 24:1523-1536(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).

    Entry informationi

    Entry nameiGCSPB_THET8
    AccessioniPrimary (citable) accession number: Q5SKW7
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 15, 2008
    Last sequence update: December 21, 2004
    Last modified: October 1, 2014
    This is version 68 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3