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P74416

- GCSP_SYNY3

UniProt

P74416 - GCSP_SYNY3

Protein

Glycine dehydrogenase (decarboxylating)

Gene

gcvP

Organism
Synechocystis sp. (strain PCC 6803 / Kazusa)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 88 (01 Oct 2014)
      Sequence version 1 (01 Feb 1997)
      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

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Glycine dehydrogenase (decarboxylating)UniRule annotation (EC:1.4.4.2UniRule annotation)
    Alternative name(s):
    Glycine cleavage system P-proteinUniRule annotation
    Glycine decarboxylaseUniRule annotation
    Glycine dehydrogenase (aminomethyl-transferring)UniRule annotation
    Gene namesi
    Name:gcvPUniRule annotation
    Ordered Locus Names:slr0293
    OrganismiSynechocystis sp. (strain PCC 6803 / Kazusa)
    Taxonomic identifieri1111708 [NCBI]
    Taxonomic lineageiBacteriaCyanobacteriaOscillatoriophycideaeChroococcalesSynechocystis
    ProteomesiUP000001425: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 983983Glycine dehydrogenase (decarboxylating)PRO_0000166942Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei726 – 7261N6-(pyridoxal phosphate)lysineUniRule annotation

    Interactioni

    Subunit structurei

    The glycine cleavage system is composed of four proteins: P, T, L and H.UniRule annotation

    Protein-protein interaction databases

    IntActiP74416. 2 interactions.
    STRINGi1148.slr0293.

    Structurei

    Secondary structure

    1
    983
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi16 – 2611
    Helixi33 – 375
    Helixi42 – 5211
    Helixi57 – 648
    Helixi67 – 693
    Helixi83 – 9412
    Helixi115 – 1206
    Turni121 – 1233
    Helixi125 – 1284
    Helixi136 – 1383
    Helixi140 – 15718
    Beta strandi160 – 1623
    Helixi169 – 18214
    Beta strandi190 – 1945
    Helixi199 – 20911
    Helixi210 – 2123
    Beta strandi215 – 2195
    Helixi221 – 2233
    Beta strandi230 – 2389
    Helixi248 – 2569
    Beta strandi260 – 2656
    Helixi269 – 2713
    Helixi276 – 2794
    Beta strandi282 – 2876
    Turni289 – 2924
    Helixi296 – 2983
    Beta strandi303 – 3075
    Helixi309 – 3146
    Beta strandi319 – 3257
    Beta strandi330 – 3356
    Helixi337 – 3393
    Helixi341 – 3444
    Helixi345 – 3473
    Helixi357 – 39539
    Beta strandi403 – 41210
    Turni415 – 4173
    Helixi418 – 42710
    Beta strandi439 – 4435
    Helixi450 – 46112
    Beta strandi463 – 4653
    Helixi471 – 4766
    Helixi483 – 4853
    Helixi495 – 4973
    Helixi503 – 51513
    Turni520 – 5223
    Turni528 – 5303
    Helixi537 – 5404
    Helixi541 – 5444
    Helixi546 – 5494
    Helixi557 – 5593
    Helixi561 – 57818
    Beta strandi581 – 5844
    Helixi590 – 60718
    Beta strandi615 – 6195
    Helixi625 – 6328
    Beta strandi636 – 6405
    Beta strandi646 – 6483
    Helixi650 – 65910
    Helixi661 – 6633
    Beta strandi664 – 6729
    Helixi682 – 69110
    Beta strandi695 – 7006
    Helixi703 – 7053
    Turni706 – 7094
    Helixi712 – 7143
    Beta strandi718 – 7225
    Turni724 – 7285
    Turni733 – 7353
    Beta strandi742 – 7443
    Helixi746 – 7494
    Beta strandi773 – 7764
    Helixi781 – 7833
    Helixi784 – 81734
    Turni818 – 8203
    Beta strandi823 – 8253
    Helixi828 – 8303
    Beta strandi836 – 8394
    Helixi841 – 8477
    Helixi851 – 86010
    Beta strandi867 – 8693
    Beta strandi875 – 8784
    Helixi886 – 90722
    Beta strandi913 – 9164
    Helixi917 – 9204
    Helixi925 – 9295
    Beta strandi935 – 9373
    Helixi939 – 9435
    Helixi947 – 9504
    Helixi963 – 9686
    Beta strandi970 – 9723
    Helixi974 – 9763

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4LGLX-ray2.00A/B1-983[»]
    4LHCX-ray1.90A/B1-983[»]
    4LHDX-ray1.80A/B1-983[»]
    ProteinModelPortaliP74416.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the GcvP family.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG1003.
    HOGENOMiHOG000239369.
    KOiK00281.
    OMAiFDSRPYS.
    OrthoDBiEOG6HMXDX.
    PhylomeDBiP74416.

    Family and domain databases

    Gene3Di3.40.640.10. 2 hits.
    HAMAPiMF_00711. GcvP.
    InterProiIPR020580. GDC-P_N.
    IPR020581. GDC_P.
    IPR003437. GDC_P_homo.
    IPR015424. PyrdxlP-dep_Trfase.
    IPR015421. PyrdxlP-dep_Trfase_major_sub1.
    [Graphical view]
    PANTHERiPTHR11773. PTHR11773. 1 hit.
    PfamiPF02347. GDC-P. 2 hits.
    [Graphical view]
    SUPFAMiSSF53383. SSF53383. 3 hits.
    TIGRFAMsiTIGR00461. gcvP. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P74416-1 [UniParc]FASTAAdd to Basket

    « Hide

    MPNLEPAVVV PTSEAIAVDL TKLEEKLAPA DSFLDRHLGP GETEQRQMLQ    50
    TLGFDTLGDL IDQAVPPAIR FPRSLQLPAS QSEYGAIAQL KSIASKNQVF 100
    RSYIGMGYYD TITPPVIQRN ILENPGWYTA YTPYQAEIAQ GRLEALLNFQ 150
    TMVMDLTGLE IANASLLDEG TAAAEAMALS YGVSKSKANA FFVAQDCHPQ 200
    TIEVIKTRAN PLGIEVIVGD HHTFSFSTSI FGALLQYPAT DGAVYDYRSF 250
    IDKAHQHQAL VTLAADPLSL TLLTPPGELG ADIAVGSTQR FGIPLGYGGP 300
    HAAYFATKAE YQRKMPGRIV GVSKDAHGNP ALRLALQTRE QHIRRDKATS 350
    NICTAQVLLA VMASMYGVYH GSTGLKNIAL RIHQLTVLLA IGLKRLNYSL 400
    NNDYFFDTLR VGVGEQSAPA ILKAAEGRGI NLRPLVPGEV GISLDETVTV 450
    QDLLDLWQVF AGKDNLPFTP EELWSEVKTS FPADLTRQSL YLQDAVFNQY 500
    HSETELLRYL HQLESKDLAL NTSMIPLGSC TMKLNATAEM MPVTWPEFGK 550
    IHPFAPAGQT EGYQILFAQL EAWLGEITGF DAISLQPNAG SQGEYAGLQV 600
    IRQYHLSRGE EQRNICLIPE SAHGTNPASA VMCGMQVVPV KCDGEGNIDV 650
    EDLTSKAEKY GDRLAALMVT YPSTHGVFEA TIGTICDIVH RFGGEVYMDG 700
    ANMNAQVGLC RPADFGADVC HLNLHKTFCI PHGGGGPGMG PIGVKSHLQA 750
    FLPRTSLNST AELQAEDQSI GMISAAPYGS ASILVISWMY IAMMGPQGLT 800
    KATEVAILSA NYMAKRLENY YPILFRGNNE LVAHECILDL RPLKKQAAIE 850
    VEDVAKRLMD FGFHAPTVSW PVLGTMMVEP TESESLGELD RFCDAMIAIY 900
    QEAQAITHGE IDPADNPLKN APHTAQSLIC GEWNHPYSQE EAAYPAPWTK 950
    QFKFWPAVGR INNTYGDRHL VCSCEGMEAY KEG 983
    Length:983
    Mass (Da):107,322
    Last modified:February 1, 1997 - v1
    Checksum:i4009367B62A2936F
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    BA000022 Genomic DNA. Translation: BAA18516.1.
    PIRiS76257.
    RefSeqiNP_441838.1. NC_000911.1.
    YP_005651898.1. NC_017277.1.
    YP_007451719.1. NC_020286.1.

    Genome annotation databases

    EnsemblBacteriaiBAA18516; BAA18516; BAA18516.
    GeneIDi952059.
    KEGGisyn:slr0293.
    syy:SYNGTS_1945.
    syz:MYO_119630.
    PATRICi23841192. VBISynSp132158_2147.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    BA000022 Genomic DNA. Translation: BAA18516.1 .
    PIRi S76257.
    RefSeqi NP_441838.1. NC_000911.1.
    YP_005651898.1. NC_017277.1.
    YP_007451719.1. NC_020286.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    4LGL X-ray 2.00 A/B 1-983 [» ]
    4LHC X-ray 1.90 A/B 1-983 [» ]
    4LHD X-ray 1.80 A/B 1-983 [» ]
    ProteinModelPortali P74416.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    IntActi P74416. 2 interactions.
    STRINGi 1148.slr0293.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai BAA18516 ; BAA18516 ; BAA18516 .
    GeneIDi 952059.
    KEGGi syn:slr0293.
    syy:SYNGTS_1945.
    syz:MYO_119630.
    PATRICi 23841192. VBISynSp132158_2147.

    Phylogenomic databases

    eggNOGi COG1003.
    HOGENOMi HOG000239369.
    KOi K00281.
    OMAi FDSRPYS.
    OrthoDBi EOG6HMXDX.
    PhylomeDBi P74416.

    Family and domain databases

    Gene3Di 3.40.640.10. 2 hits.
    HAMAPi MF_00711. GcvP.
    InterProi IPR020580. GDC-P_N.
    IPR020581. GDC_P.
    IPR003437. GDC_P_homo.
    IPR015424. PyrdxlP-dep_Trfase.
    IPR015421. PyrdxlP-dep_Trfase_major_sub1.
    [Graphical view ]
    PANTHERi PTHR11773. PTHR11773. 1 hit.
    Pfami PF02347. GDC-P. 2 hits.
    [Graphical view ]
    SUPFAMi SSF53383. SSF53383. 3 hits.
    TIGRFAMsi TIGR00461. gcvP. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions."
      Kaneko T., Sato S., Kotani H., Tanaka A., Asamizu E., Nakamura Y., Miyajima N., Hirosawa M., Sugiura M., Sasamoto S., Kimura T., Hosouchi T., Matsuno A., Muraki A., Nakazaki N., Naruo K., Okumura S., Shimpo S.
      , Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Tabata S.
      DNA Res. 3:109-136(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: PCC 6803 / Kazusa.

    Entry informationi

    Entry nameiGCSP_SYNY3
    AccessioniPrimary (citable) accession number: P74416
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: September 19, 2003
    Last sequence update: February 1, 1997
    Last modified: October 1, 2014
    This is version 88 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
    3. Synechocystis PCC 6803
      Synechocystis (strain PCC 6803): entries and gene names

    External Data

    Dasty 3