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Protein

Glycine dehydrogenase (decarboxylating)

Gene

gcvP

Organism
Xylella fastidiosa (strain 9a5c)
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

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:XF_1385
OrganismiXylella fastidiosa (strain 9a5c)
Taxonomic identifieri160492 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaXanthomonadalesXanthomonadaceaeXylella
ProteomesiUP000000812 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 993993Glycine dehydrogenase (decarboxylating)PRO_0000166950Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei715 – 7151N6-(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

STRINGi160492.XF1385.

Structurei

3D structure databases

ProteinModelPortaliQ9PDJ4.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the GcvP family.UniRule annotation

Phylogenomic databases

eggNOGiCOG1003.
KOiK00281.
OMAiPHYKTLY.
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.

Q9PDJ4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MFSVSHFCSG SLMMSHTLSS LRDLEYQGAF VERHIGPNDV EIAQMLRVVG
60 70 80 90 100
YDSLESLTDA IVPEKIRSTV ALDLPKGITE EEALAKIRVI ANKNRVFRSF
110 120 130 140 150
IGQGYYGTHT PKVILRNVLE NPAWYTAYTP YQAEISQGRM EALINFQTMC
160 170 180 190 200
ADLTGMEIAN ASLLDEATAA AEAMSLAKRS AKSRSDLFFV HDAVHPQTLE
210 220 230 240 250
LLRTRAEPLG IVLRVGTPEE ALQADVFGIL LQYPDTFGRI GDHRVLADAV
260 270 280 290 300
HARGGLVAVA SDLLALTLIT PPGEWGADIV VGNSQRFGVP FGFGGPHAGF
310 320 330 340 350
MACRDIYKRS IPGRLIGVSV DAAGHPAYRL ALQTREQHIR REKATSNICT
360 370 380 390 400
AQVLLAVMAS MYAVYHGPQG LLRIAWRTHR MAAILAAALR GAGLTVGEYF
410 420 430 440 450
FDTLHIVGID AVAIHCAAAA AGMNLRMIDN AQLGISLDET VTRSDVVALG
460 470 480 490 500
QVFGVQVDVE ALDAITADAL PAGLLRSSAF LTHPVFNTHH SEHELLRYLR
510 520 530 540 550
MLADKDLAMD RTMIPLGSCT MKLNATAEMI PVTWQEFACI HPLAPAVQWS
560 570 580 590 600
GYRQLIDELE AMLAECTGYD AISLQPNSGA QGEYAGLLAI RAYHRSRGEE
610 620 630 640 650
RRNVCLIPES AHGTNPASAQ LCGMQVVIIK CDRSGNVDVD DLRMKAEKYS
660 670 680 690 700
DSLAALMVTY PSTHGVFEEA ITEICEIVHA HGGQVYTDGA NMNALVGVAK
710 720 730 740 750
PGRWGSDVSH LNLHKTFCIP HGGGGPGVGP CAVKAHLAPF LPKTLPLPGD
760 770 780 790 800
AAGLPVQGTQ EAKVGMVSAA NFGSASILPV SWMYITMMGA AGLRKATQVA
810 820 830 840 850
LLNANYIAKR LAPHYKTLYT GRHGLVAHEC ILDVRPLEKV SGVSAEDIAK
860 870 880 890 900
RLIDFGFHAP TLSFPVAGTL MVEPTESESQ QELDRFVDAM IQIRGEIAAI
910 920 930 940 950
EKGHLDPEDN PLKQAPHTAV QVMASQWGHA YSRELAAFPL GVLHHAKYWP
960 970 980 990
PVARVDNVYG DKHVMCACIP VEAYKEKEDS EIQHLIEEDA SRC
Length:993
Mass (Da):107,648
Last modified:October 1, 2000 - v1
Checksum:i118088B388967C46
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE003849 Genomic DNA. Translation: AAF84194.1.
PIRiC82687.
RefSeqiNP_298674.1. NC_002488.3.
WP_010893889.1. NC_002488.3.

Genome annotation databases

EnsemblBacteriaiAAF84194; AAF84194; XF_1385.
KEGGixfa:XF1385.
PATRICi24132871. VBIXylFas578_1464.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE003849 Genomic DNA. Translation: AAF84194.1.
PIRiC82687.
RefSeqiNP_298674.1. NC_002488.3.
WP_010893889.1. NC_002488.3.

3D structure databases

ProteinModelPortaliQ9PDJ4.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi160492.XF1385.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAF84194; AAF84194; XF_1385.
KEGGixfa:XF1385.
PATRICi24132871. VBIXylFas578_1464.

Phylogenomic databases

eggNOGiCOG1003.
KOiK00281.
OMAiPHYKTLY.
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.
ProtoNetiSearch...

Publicationsi

  1. "The genome sequence of the plant pathogen Xylella fastidiosa."
    Simpson A.J.G., Reinach F.C., Arruda P., Abreu F.A., Acencio M., Alvarenga R., Alves L.M.C., Araya J.E., Baia G.S., Baptista C.S., Barros M.H., Bonaccorsi E.D., Bordin S., Bove J.M., Briones M.R.S., Bueno M.R.P., Camargo A.A., Camargo L.E.A.
    , Carraro D.M., Carrer H., Colauto N.B., Colombo C., Costa F.F., Costa M.C.R., Costa-Neto C.M., Coutinho L.L., Cristofani M., Dias-Neto E., Docena C., El-Dorry H., Facincani A.P., Ferreira A.J.S., Ferreira V.C.A., Ferro J.A., Fraga J.S., Franca S.C., Franco M.C., Frohme M., Furlan L.R., Garnier M., Goldman G.H., Goldman M.H.S., Gomes S.L., Gruber A., Ho P.L., Hoheisel J.D., Junqueira M.L., Kemper E.L., Kitajima J.P., Krieger J.E., Kuramae E.E., Laigret F., Lambais M.R., Leite L.C.C., Lemos E.G.M., Lemos M.V.F., Lopes S.A., Lopes C.R., Machado J.A., Machado M.A., Madeira A.M.B.N., Madeira H.M.F., Marino C.L., Marques M.V., Martins E.A.L., Martins E.M.F., Matsukuma A.Y., Menck C.F.M., Miracca E.C., Miyaki C.Y., Monteiro-Vitorello C.B., Moon D.H., Nagai M.A., Nascimento A.L.T.O., Netto L.E.S., Nhani A. Jr., Nobrega F.G., Nunes L.R., Oliveira M.A., de Oliveira M.C., de Oliveira R.C., Palmieri D.A., Paris A., Peixoto B.R., Pereira G.A.G., Pereira H.A. Jr., Pesquero J.B., Quaggio R.B., Roberto P.G., Rodrigues V., de Rosa A.J.M., de Rosa V.E. Jr., de Sa R.G., Santelli R.V., Sawasaki H.E., da Silva A.C.R., da Silva A.M., da Silva F.R., Silva W.A. Jr., da Silveira J.F., Silvestri M.L.Z., Siqueira W.J., de Souza A.A., de Souza A.P., Terenzi M.F., Truffi D., Tsai S.M., Tsuhako M.H., Vallada H., Van Sluys M.A., Verjovski-Almeida S., Vettore A.L., Zago M.A., Zatz M., Meidanis J., Setubal J.C.
    Nature 406:151-159(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 9a5c.

Entry informationi

Entry nameiGCSP_XYLFA
AccessioniPrimary (citable) accession number: Q9PDJ4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 19, 2003
Last sequence update: October 1, 2000
Last modified: April 1, 2015
This is version 79 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.