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P74416

- GCSP_SYNY3

UniProt

P74416 - GCSP_SYNY3

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Protein
Glycine dehydrogenase (decarboxylating)
Gene
gcvP, slr0293
Organism
Synechocystis sp. (strain PCC 6803 / Kazusa)
Status
Reviewed - Annotation score: 3 out of 5 - Experimental evidence at protein leveli

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 By similarity.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 By similarity.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
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Ligandi

Pyridoxal phosphate

Names & Taxonomyi

Protein namesi
Recommended name:
Glycine dehydrogenase (decarboxylating) (EC:1.4.4.2)
Alternative name(s):
Glycine cleavage system P-protein
Glycine decarboxylase
Glycine dehydrogenase (aminomethyl-transferring)
Gene namesi
Name:gcvP
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)UniRule annotation
PRO_0000166942Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei726 – 7261N6-(pyridoxal phosphate)lysine By similarity

Interactioni

Subunit structurei

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

Protein-protein interaction databases

IntActiP74416. 2 interactions.
STRINGi1148.slr0293.

Structurei

Secondary structure

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.

Family & Domainsi

Sequence similaritiesi

Belongs to the GcvP family.

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: July 9, 2014
This is version 87 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

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