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Protein

Probable glycine dehydrogenase (decarboxylating) subunit 2

Gene

gcvPB

Organism
Nitrosococcus oceani (strain ATCC 19707 / NCIMB 11848)
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

BioCyciNOCE323261:GCI3-2591-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:Noc_2547
OrganismiNitrosococcus oceani (strain ATCC 19707 / NCIMB 11848)
Taxonomic identifieri323261 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaChromatialesChromatiaceaeNitrosococcus
ProteomesiUP000006838 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 486486Probable glycine dehydrogenase (decarboxylating) subunit 2PRO_1000045701Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei264 – 2641N6-(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

STRINGi323261.Noc_2547.

Structurei

3D structure databases

ProteinModelPortaliQ3J846.
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.
InterProiIPR023012. GcvPB.
IPR020580. GDC-P_N.
IPR020581. GDC_P.
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.

Q3J846-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLIFESSRPG RQARAQAPKP TAATNDLPER FLRQQPPALP EVSEMDVVRH
60 70 80 90 100
YTGLSQKNFS IDTHFYPLGS CTMKYNPRAC HTLASLPGFL ERHPATPEAM
110 120 130 140 150
SQGFLACLYE LQDILAKMTG MQTMSLAPMA GAQGEFTGVA MIRAYHEARG
160 170 180 190 200
DKERCEMLVP DAAHGTNPAT ATMCGFRVRE IPTNPEGDVD LEALHKALGP
210 220 230 240 250
QTAGIMLTNP STLGIFDRNI QVIAQSVHKA GGLLYYDGAN LNAILGKVKP
260 270 280 290 300
GDMGFDVIHL NLHKTFSTPH GGGGPGSGPV GVGEKLLPFL PVPRVARAEG
310 320 330 340 350
GSYRWLTAED CPQTIGPLSA WMGNAGVLLR AYIYVRLLGL EGMKRVADFS
360 370 380 390 400
ALNANYLAQR MAEAGFDLAY PMRRAGHEFV VTLKRQAKEL GVTATDFAKR
410 420 430 440 450
LLDLGFHAPT IYFPLLVPEC LLIEPAETES KQTLDAFVAA MEQIAKEAQE
460 470 480
NPELLKQAPH TLPARRLDEV KAAKELDLAW KPTPHE
Length:486
Mass (Da):52,987
Last modified:November 8, 2005 - v1
Checksum:iEE8049AD0A7DE8AC
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000127 Genomic DNA. Translation: ABA59000.1.
RefSeqiYP_344530.1. NC_007484.1.

Genome annotation databases

EnsemblBacteriaiABA59000; ABA59000; Noc_2547.
KEGGinoc:Noc_2547.
PATRICi22709538. VBINitOce57959_2973.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000127 Genomic DNA. Translation: ABA59000.1.
RefSeqiYP_344530.1. NC_007484.1.

3D structure databases

ProteinModelPortaliQ3J846.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi323261.Noc_2547.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABA59000; ABA59000; Noc_2547.
KEGGinoc:Noc_2547.
PATRICi22709538. VBINitOce57959_2973.

Phylogenomic databases

eggNOGiCOG1003.
HOGENOMiHOG000239368.
KOiK00283.
OMAiMHINLHK.
OrthoDBiEOG6HMXDX.

Enzyme and pathway databases

BioCyciNOCE323261:GCI3-2591-MONOMER.

Family and domain databases

Gene3Di3.40.640.10. 2 hits.
HAMAPiMF_00713. GcvPB.
InterProiIPR023012. GcvPB.
IPR020580. GDC-P_N.
IPR020581. GDC_P.
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. "Complete genome sequence of the marine, chemolithoautotrophic, ammonia-oxidizing bacterium Nitrosococcus oceani ATCC 19707."
    Klotz M.G., Arp D.J., Chain P.S.G., El-Sheikh A.F., Hauser L.J., Hommes N.G., Larimer F.W., Malfatti S.A., Norton J.M., Poret-Peterson A.T., Vergez L.M., Ward B.B.
    Appl. Environ. Microbiol. 72:6299-6315(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 19707 / NCIMB 11848.

Entry informationi

Entry nameiGCSPB_NITOC
AccessioniPrimary (citable) accession number: Q3J846
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: November 8, 2005
Last modified: April 29, 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.