ID X5DI12_9BACT Unreviewed; 958 AA.
AC X5DI12;
DT 11-JUN-2014, integrated into UniProtKB/TrEMBL.
DT 11-JUN-2014, sequence version 1.
DT 27-MAR-2024, entry version 51.
DE RecName: Full=Glycine dehydrogenase (decarboxylating) {ECO:0000256|HAMAP-Rule:MF_00711};
DE EC=1.4.4.2 {ECO:0000256|HAMAP-Rule:MF_00711};
DE AltName: Full=Glycine cleavage system P-protein {ECO:0000256|HAMAP-Rule:MF_00711};
DE AltName: Full=Glycine decarboxylase {ECO:0000256|HAMAP-Rule:MF_00711};
DE AltName: Full=Glycine dehydrogenase (aminomethyl-transferring) {ECO:0000256|HAMAP-Rule:MF_00711};
GN Name=gcvP {ECO:0000256|HAMAP-Rule:MF_00711};
GN ORFNames=SAMN05444285_104125 {ECO:0000313|EMBL:SES99243.1};
OS Draconibacterium orientale.
OC Bacteria; Bacteroidota; Bacteroidia; Marinilabiliales; Prolixibacteraceae;
OC Draconibacterium.
OX NCBI_TaxID=1168034 {ECO:0000313|EMBL:SES99243.1, ECO:0000313|Proteomes:UP000181981};
RN [1] {ECO:0000313|EMBL:SES99243.1, ECO:0000313|Proteomes:UP000181981}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 25947 {ECO:0000313|EMBL:SES99243.1,
RC ECO:0000313|Proteomes:UP000181981};
RA de Groot N.N.;
RL Submitted (OCT-2016) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: The glycine cleavage system catalyzes the degradation of
CC glycine. The P protein binds the alpha-amino group of glycine through
CC its pyridoxal phosphate cofactor; CO(2) is released and the remaining
CC methylamine moiety is then transferred to the lipoamide cofactor of the
CC H protein. {ECO:0000256|ARBA:ARBA00003788, ECO:0000256|HAMAP-
CC Rule:MF_00711}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=glycine + H(+) + N(6)-[(R)-lipoyl]-L-lysyl-[glycine-cleavage
CC complex H protein] = CO2 + N(6)-[(R)-S(8)-aminomethyldihydrolipoyl]-
CC L-lysyl-[glycine-cleavage complex H protein]; Xref=Rhea:RHEA:24304,
CC Rhea:RHEA-COMP:10494, Rhea:RHEA-COMP:10495, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16526, ChEBI:CHEBI:57305, ChEBI:CHEBI:83099,
CC ChEBI:CHEBI:83143; EC=1.4.4.2;
CC Evidence={ECO:0000256|ARBA:ARBA00043839, ECO:0000256|HAMAP-
CC Rule:MF_00711};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000256|ARBA:ARBA00001933,
CC ECO:0000256|HAMAP-Rule:MF_00711, ECO:0000256|PIRSR:PIRSR603437-50};
CC -!- SUBUNIT: The glycine cleavage system is composed of four proteins: P,
CC T, L and H. {ECO:0000256|ARBA:ARBA00011690, ECO:0000256|HAMAP-
CC Rule:MF_00711}.
CC -!- SIMILARITY: Belongs to the GcvP family. {ECO:0000256|ARBA:ARBA00010756,
CC ECO:0000256|HAMAP-Rule:MF_00711}.
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DR EMBL; FOHT01000004; SES99243.1; -; Genomic_DNA.
DR RefSeq; WP_038558751.1; NZ_FOHT01000004.1.
DR AlphaFoldDB; X5DI12; -.
DR STRING; 1168034.FH5T_12385; -.
DR GeneID; 78098714; -.
DR eggNOG; COG0403; Bacteria.
DR eggNOG; COG1003; Bacteria.
DR HOGENOM; CLU_004620_3_0_10; -.
DR OrthoDB; 9801272at2; -.
DR Proteomes; UP000181981; Unassembled WGS sequence.
DR GO; GO:0004375; F:glycine dehydrogenase (decarboxylating) activity; IEA:UniProtKB-EC.
DR GO; GO:0019464; P:glycine decarboxylation via glycine cleavage system; IEA:UniProtKB-UniRule.
DR CDD; cd00613; GDC-P; 2.
DR Gene3D; 3.90.1150.10; Aspartate Aminotransferase, domain 1; 2.
DR Gene3D; 3.40.640.10; Type I PLP-dependent aspartate aminotransferase-like (Major domain); 2.
DR HAMAP; MF_00711; GcvP; 1.
DR InterPro; IPR003437; GcvP.
DR InterPro; IPR049316; GDC-P_C.
DR InterPro; IPR049315; GDC-P_N.
DR InterPro; IPR020581; GDC_P.
DR InterPro; IPR015424; PyrdxlP-dep_Trfase.
DR InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
DR InterPro; IPR015422; PyrdxlP-dep_Trfase_small.
DR NCBIfam; TIGR00461; gcvP; 1.
DR PANTHER; PTHR11773:SF1; GLYCINE DEHYDROGENASE (DECARBOXYLATING), MITOCHONDRIAL; 1.
DR PANTHER; PTHR11773; GLYCINE DEHYDROGENASE, DECARBOXYLATING; 1.
DR Pfam; PF21478; GcvP2_C; 1.
DR Pfam; PF02347; GDC-P; 2.
DR SUPFAM; SSF53383; PLP-dependent transferases; 2.
PE 3: Inferred from homology;
KW Oxidoreductase {ECO:0000256|ARBA:ARBA00023002, ECO:0000256|HAMAP-
KW Rule:MF_00711};
KW Pyridoxal phosphate {ECO:0000256|HAMAP-Rule:MF_00711,
KW ECO:0000256|PIRSR:PIRSR603437-50}.
FT DOMAIN 9..439
FT /note="Glycine cleavage system P-protein N-terminal"
FT /evidence="ECO:0000259|Pfam:PF02347"
FT DOMAIN 469..731
FT /note="Glycine cleavage system P-protein N-terminal"
FT /evidence="ECO:0000259|Pfam:PF02347"
FT DOMAIN 775..896
FT /note="Glycine dehydrogenase C-terminal"
FT /evidence="ECO:0000259|Pfam:PF21478"
FT MOD_RES 704
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00711,
FT ECO:0000256|PIRSR:PIRSR603437-50"
SQ SEQUENCE 958 AA; 106518 MW; 9E5863B04C39502E CRC64;
MSQDRFVTRH IGPRGVEIAE MLEYVGVSSM EELLEQTVPS NIRLQQPLKM KEGLSERKYF
RRILELASMN KVFNTYIGMG YYDTITPAVV LRNVLENPVW YTSYTPYQAE ISQGRLEALL
NFQTMVCGLT GMDIANASLL DEATAAAEAM VMMANLRSRK MVKAGMNTIL VDEKMWPQTH
DVLKTRALPL GFELKIQPKD EFNFDENVFG VIVQYPNSDG EITDYAELVE KAHEKEIKVA
VAADLMSLAI LMPPGEWGAD IVFGNSQRFG VPMGYGGPHA AFFAAREEFK RNMPGRIIGV
TKDIHGNRAL RMALQTREQH IKREKATSNI CTAQALLAIM AGFFGVYHGP EGVIGIAERI
HNIAAFLAIE IEKLGYTQIN KNFFDTIRFA LPKHVMREDI EWLSLELEMN FRYFENGDVG
ISIDETTNPQ DIGWIIEVFA KAANKKWQVA EEYPEGFEID AAFKRTSKFM TEEVFNKYRS
ETEMVRYIKR LAKKDISLTQ SMISLGSCTM KLNAATEMLP LSWIEFNGLH PFVPKNQARG
YHEMMEELRR DLSEITGMAD VSLQPNSGAA GEYAGLMVIQ EYHKSRGEGQ RDVVIIPSSA
HGTNPASAVM AGTKVVVVKC DEKGNVDMDD LRAKAELHKD RLSAFMVTYP STHGVFEASI
IEMCEVIHEN GGQVYMDGAN MNAQVGLTNP RLIGADVCHL NLHKTFAIPH GGGGPGVGPI
GVASHLVEFL PSHPIMNNGH VGITAVSAAP WGSASVLPIT YGYIKMMGAE GLTEATKLAI
LNANYIATAL KDNYGILYTG ENGRVAHELI LECRHLKASA GITEEDIAKR LMDYGFHAPT
LSFPVHGTLM IEPTESESKD ELDRFISALN SIFEEVKEVE NGVADKADNV LKNAPHTAQS
VCADEWTHAY GREKAAYPLD WVRENKYWVP VGRVDNAWGD RNLICTCGSP EEYEAFAD
//
