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C5CRW8

- GCSP_VARPS

UniProt

C5CRW8 - GCSP_VARPS

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Protein

Glycine dehydrogenase (decarboxylating)

Gene

gcvP

Organism
Variovorax paradoxus (strain S110)
Status
Reviewed - 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

BioCyciVPAR543728:GHLL-3332-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:Vapar_3301
OrganismiVariovorax paradoxus (strain S110)
Taxonomic identifieri543728 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesComamonadaceaeVariovorax
ProteomesiUP000000453: Chromosome 1

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 968968Glycine dehydrogenase (decarboxylating)PRO_1000212658Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei713 – 7131N6-(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

STRINGi543728.Vapar_3301.

Structurei

3D structure databases

ProteinModelPortaliC5CRW8.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the GcvP family.UniRule annotation

Phylogenomic databases

eggNOGiCOG1003.
HOGENOMiHOG000239369.
KOiK00281.
OMAiFDSRPYS.
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.

C5CRW8-1 [UniParc]FASTAAdd to Basket

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        10         20         30         40         50
MPIPALPSLQ QLENAEEFLA RHIGIDAADE ARMLPVIGSE TRAELIDGIV
60 70 80 90 100
PAAIRRAKPM RLPAPATEAD ALAELKAIAA KNKVFRSFIG QGYYGTHTPG
110 120 130 140 150
VILRNVLENP AWYTAYTPYQ AEISQGRMEA LLNFQTMVCD LTGMAIANAS
160 170 180 190 200
MLDEATAAAE AMTLAKRSVK SKSNVFLVSG DCHPQTIEVI KTRAAPLGIE
210 220 230 240 250
VKVSTVSETL PHLMVSGEFF GVLAQYPATT GHVHDLRPLA GHAHQCDAAF
260 270 280 290 300
CVAADLLALT LLAPPGEWDA DIVCGTTQRF GMPMCNGGPH AAYLACRDEF
310 320 330 340 350
KRSLPGRLVG VSVDTHGQPA YRLALQTREQ HIRREKATSN ICTAQVLPAV
360 370 380 390 400
VASMYAVYHG PDGLTRIAQR VAALTAILAQ GLAQMGREPV NGTAFDSLTI
410 420 430 440 450
RTGDDTPKII ERAQAAGVNL RQRLQQHLGI SLDETTTRAD IETLWALFVP
460 470 480 490 500
AGTPMPRFDD LANAVPRLPE DLRRTSAFLT HPVFNTHKSE TAMLRYIRSL
510 520 530 540 550
SDKDLALDRS MIPLGSCTMK LNATSEMIPI TWPEFANIHP FAPAEQLVGY
560 570 580 590 600
AQLDAQLRAW LCEATGYAGI SLQPNAGSQG EYAGLLAIRS FHEANGQGHR
610 620 630 640 650
NICLIPSSAH GTNPASAQMV GLQVVVTACD AQGNVDMDDL RRACEKHSDK
660 670 680 690 700
LAAVMITYPS THGVFETRVK ELCELVHEHG GRVYVDGANM NALVGVAAPG
710 720 730 740 750
EFGGDVSHLN LHKTFCIPHG GGGPGVGPVC VVEDLVPYLP GHATAGVASN
760 770 780 790 800
GVGAVSAAPL GNAAVLPISW MYCRMMGAKG LQAATEIAIL SANYISARLK
810 820 830 840 850
DHYPTLYASP NGHVAHECIL DLRPLKDSSG VTAEDVAKRL IDYGFHAPTL
860 870 880 890 900
SFPVPGTLMV EPTESEPLAE LDRFIDAMIA IRGEIRRVEE GVWPKDDNPL
910 920 930 940 950
KHAPHTAASL MAAEWPHPYS RELGAFPLAE LKLAKYWPPI GRVDNVYGDR
960
NLFCSCVPVG DYKETEEA
Length:968
Mass (Da):104,204
Last modified:July 28, 2009 - v1
Checksum:i8DFF68ABC656715D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001635 Genomic DNA. Translation: ACS19919.1.
RefSeqiYP_002945185.1. NC_012791.1.

Genome annotation databases

EnsemblBacteriaiACS19919; ACS19919; Vapar_3301.
GeneIDi7973697.
KEGGivap:Vapar_3301.
PATRICi24007035. VBIVarPar36677_3304.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001635 Genomic DNA. Translation: ACS19919.1 .
RefSeqi YP_002945185.1. NC_012791.1.

3D structure databases

ProteinModelPortali C5CRW8.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 543728.Vapar_3301.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ACS19919 ; ACS19919 ; Vapar_3301 .
GeneIDi 7973697.
KEGGi vap:Vapar_3301.
PATRICi 24007035. VBIVarPar36677_3304.

Phylogenomic databases

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

Enzyme and pathway databases

BioCyci VPAR543728:GHLL-3332-MONOMER.

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. "Complete genome sequence of the metabolically versatile plant growth-promoting endophyte, Variovorax paradoxus S110."
    Han J.I., Choi H.K., Lee S.W., Orwin P.M., Kim J., Laroe S.L., Kim T.G., O'Neil J., Leadbetter J.R., Lee S.Y., Hur C.G., Spain J.C., Ovchinnikova G., Goodwin L., Han C.
    J. Bacteriol. 193:1183-1190(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: S110.

Entry informationi

Entry nameiGCSP_VARPS
AccessioniPrimary (citable) accession number: C5CRW8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 22, 2009
Last sequence update: July 28, 2009
Last modified: November 26, 2014
This is version 39 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