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Protein

Probable glycine dehydrogenase (decarboxylating) subunit 2

Gene

gcvPB

Organism
Syntrophomonas wolfei subsp. wolfei (strain DSM 2245B / Goettingen)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

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 5'-phosphateUniRule 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

Enzyme and pathway databases

BioCyciSWOL335541:GHL1-2034-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:Swol_1980
OrganismiSyntrophomonas wolfei subsp. wolfei (strain DSM 2245B / Goettingen)
Taxonomic identifieri335541 [NCBI]
Taxonomic lineageiBacteriaFirmicutesClostridiaClostridialesSyntrophomonadaceaeSyntrophomonas
ProteomesiUP000001968 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 486486Probable glycine dehydrogenase (decarboxylating) subunit 2PRO_1000083235Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei269 – 2691N6-(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

STRINGi335541.Swol_1980.

Structurei

3D structure databases

ProteinModelPortaliQ0AVH9.
SMRiQ0AVH9. Positions 3-481.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG1003.
HOGENOMiHOG000239368.
KOiK00283.
OMAiMHINLHK.
OrthoDBiEOG6HMXDX.

Family and domain databases

Gene3Di3.40.640.10. 2 hits.
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.

Q0AVH9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSKVIFARSV AGGGGFFLPP CDVAEIEPAA EINPEFLRAE APLLPELSEV
60 70 80 90 100
EVVRHYVELS QRAYGVDNGF YPLGSCTMKY NPKINEWAAR LPGFANLHPY
110 120 130 140 150
QPEESVQGAL ELLYRAEKLC CEIGGMDRFT LQPAAGAHGE LTGLMIIKAY
160 170 180 190 200
HQHRQDLART KILVPDSAHG TNPATAHVLG FEVVEVKSNE EGLVDLQDLK
210 220 230 240 250
ACMSSEVAGL MLTNPNTLGL FEKEIEEIAT VVHADGGLLY YDGANLNGIV
260 270 280 290 300
GVARPGDMGF DVLHFNLHKT FGTPHGGGGP GSGPVGVKDF LSGFLPHPLV
310 320 330 340 350
EKKEEGYYLD YDRPLSIGKV RSFYGNFGVI VKAYAYMMAL GGPGLREACE
360 370 380 390 400
LAVLNSNYLR HHLQEDYHIP FNRLCKHEFV ASGQKQLAEN GVSTLDIAKR
410 420 430 440 450
LMDYGFHPPT VYFPLIVKEA LMIEPVETES RERLDEFIAA MREIAREARE
460 470 480
NPDILHQAPH STVIKRVDEV RAARQPILRW PGLGAE
Length:486
Mass (Da):53,556
Last modified:October 16, 2006 - v1
Checksum:i071C008DEAAD060A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000448 Genomic DNA. Translation: ABI69275.1.
RefSeqiWP_011641367.1. NC_008346.1.
YP_754646.1. NC_008346.1.

Genome annotation databases

EnsemblBacteriaiABI69275; ABI69275; Swol_1980.
KEGGiswo:Swol_1980.
PATRICi23859003. VBISynWol51738_2139.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000448 Genomic DNA. Translation: ABI69275.1.
RefSeqiWP_011641367.1. NC_008346.1.
YP_754646.1. NC_008346.1.

3D structure databases

ProteinModelPortaliQ0AVH9.
SMRiQ0AVH9. Positions 3-481.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi335541.Swol_1980.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABI69275; ABI69275; Swol_1980.
KEGGiswo:Swol_1980.
PATRICi23859003. VBISynWol51738_2139.

Phylogenomic databases

eggNOGiCOG1003.
HOGENOMiHOG000239368.
KOiK00283.
OMAiMHINLHK.
OrthoDBiEOG6HMXDX.

Enzyme and pathway databases

BioCyciSWOL335541:GHL1-2034-MONOMER.

Family and domain databases

Gene3Di3.40.640.10. 2 hits.
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.
ProtoNetiSearch...

Publicationsi

  1. "The genome of Syntrophomonas wolfei: new insights into syntrophic metabolism and biohydrogen production."
    Sieber J.R., Sims D.R., Han C., Kim E., Lykidis A., Lapidus A.L., McDonnald E., Rohlin L., Culley D.E., Gunsalus R., McInerney M.J.
    Environ. Microbiol. 12:2289-2301(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: DSM 2245B / Goettingen.

Entry informationi

Entry nameiGCSPB_SYNWW
AccessioniPrimary (citable) accession number: Q0AVH9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 19, 2008
Last sequence update: October 16, 2006
Last modified: March 31, 2015
This is version 64 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

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.