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Protein

Glycine dehydrogenase (decarboxylating)

Gene

gcvP

Organism
Sinorhizobium medicae (strain WSM419) (Ensifer medicae)
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

BioCyciSMED366394:GJAL-1203-MONOMER.

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:Smed_1182
OrganismiSinorhizobium medicae (strain WSM419) (Ensifer medicae)
Taxonomic identifieri366394 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesRhizobiaceaeSinorhizobium/Ensifer groupSinorhizobium
ProteomesiUP000001108 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 954954Glycine dehydrogenase (decarboxylating)PRO_1000045620Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei704 – 7041N6-(pyridoxal phosphate)lysineUniRule annotation

Proteomic databases

PRIDEiA6U8Q3.

Interactioni

Subunit structurei

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

Protein-protein interaction databases

STRINGi366394.Smed_1182.

Structurei

3D structure databases

ProteinModelPortaliA6U8Q3.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the GcvP family.UniRule annotation

Phylogenomic databases

eggNOGiCOG1003.
HOGENOMiHOG000239369.
KOiK00281.
OMAiRAESEMT.
OrthoDBiEOG6HMXDX.

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.

A6U8Q3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSMPKDFTFT DYKPYDFANR RHIGPSPAEM DEMLKVVGYP SLDALIDDTV
60 70 80 90 100
PPSIRQQTPL AWGAPMTERE ALDKLRETAN RNRKVVSLIG QGYYGTITPP
110 120 130 140 150
VIQRNILENP AWYTAYTPYQ PEISQGRLEA LLNFQTMVCD LTGLDVANAS
160 170 180 190 200
LLDEATAAAE AMAIAERVAK SKAKAFFVDE NCHPQTIALL KTRAEPLGWQ
210 220 230 240 250
IVVGNPFEDL DAAIVFGAIF QYPGTYGHVR DFSGLIARLH ELGAIAAVAA
260 270 280 290 300
DPLALALLKS PGEMGADIAV GSTQRFGVPV GYGGPHAAYM AVRDAYKRSM
310 320 330 340 350
PGRLVGVSVD ARGNRAYRLS LQTREQHIRR EKATSNICTA QVLLAVMASM
360 370 380 390 400
YAVFHGPEGI KAIAQSVHQK TVRLALGLEK LGYTVEPDVF FDTITVEVGK
410 420 430 440 450
LQGIILKAAV AEDVNLRKIG TTKIGISLDE RSRPITLEAV WRAFGGDFSV
460 470 480 490 500
DQFEPDYRLP KELLRTSDYL THPIFHMNRA ESEMTRYMRR LADRDLALDR
510 520 530 540 550
AMIPLGSCTM KLNATAEMLP ITWPEFSEIH PFVPADQAMG YHHLIEDLSQ
560 570 580 590 600
KLCAITGYDA ISMQPNSGAQ GEYAGLLAIR AYHIANGNEH RDVCLIPTSA
610 620 630 640 650
HGTNPASAQM AGMKVVVVKV SDAGEIAMDD FRAKAEQYAE TLSCCMITYP
660 670 680 690 700
STHGVFEENV REVCEIVHKH GGQVYLDGAN MNAMVGLSRP GDIGSDVSHL
710 720 730 740 750
NLHKTFCIPH GGGGPGMGPI GVKAHLAPFL PGHPESGEHK GAVSAAPFGS
760 770 780 790 800
ASILPISWSY CLMMGGEGLT QATKVAILNA NYVAARLKGA FDVLYKSAKG
810 820 830 840 850
RVAHECIIDT RPLAESAGVT VDDVAKRLID CGFHAPTMSW PVAGTLMIEP
860 870 880 890 900
TESETKAELD RFCDALLAIR EEARAIAEGR MDKINNPLKN APHTVEDLVG
910 920 930 940 950
DWDRPYSREQ ACFPPGAFRV DKYWSPVNRV DNVYGDRNLV CTCPPIESYA

EAAE
Length:954
Mass (Da):104,061
Last modified:August 20, 2007 - v1
Checksum:i9A09A8613FE27986
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000738 Genomic DNA. Translation: ABR60033.1.
RefSeqiYP_001326868.1. NC_009636.1.

Genome annotation databases

EnsemblBacteriaiABR60033; ABR60033; Smed_1182.
GeneIDi5322029.
KEGGismd:Smed_1182.
PATRICi23621318. VBISinMed134228_4310.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000738 Genomic DNA. Translation: ABR60033.1.
RefSeqiYP_001326868.1. NC_009636.1.

3D structure databases

ProteinModelPortaliA6U8Q3.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi366394.Smed_1182.

Proteomic databases

PRIDEiA6U8Q3.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABR60033; ABR60033; Smed_1182.
GeneIDi5322029.
KEGGismd:Smed_1182.
PATRICi23621318. VBISinMed134228_4310.

Phylogenomic databases

eggNOGiCOG1003.
HOGENOMiHOG000239369.
KOiK00281.
OMAiRAESEMT.
OrthoDBiEOG6HMXDX.

Enzyme and pathway databases

BioCyciSMED366394:GJAL-1203-MONOMER.

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.
ProtoNetiSearch...

Publicationsi

  1. "Complete sequence of Sinorhizobium medicae WSM419 chromosome."
    US DOE Joint Genome Institute
    Copeland A., Lucas S., Lapidus A., Barry K., Glavina del Rio T., Dalin E., Tice H., Pitluck S., Chain P., Malfatti S., Shin M., Vergez L., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N., Reeve W.G., Richardson P.
    Submitted (MAY-2007) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: WSM419.

Entry informationi

Entry nameiGCSP_SINMW
AccessioniPrimary (citable) accession number: A6U8Q3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 14, 2008
Last sequence update: August 20, 2007
Last modified: January 6, 2015
This is version 54 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

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.