GCSPB_THET8
ID GCSPB_THET8 Reviewed; 474 AA.
AC Q5SKW7;
DT 15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT 21-DEC-2004, sequence version 1.
DT 25-MAY-2022, entry version 96.
DE RecName: Full=Probable glycine dehydrogenase (decarboxylating) subunit 2 {ECO:0000255|HAMAP-Rule:MF_00713};
DE EC=1.4.4.2 {ECO:0000255|HAMAP-Rule:MF_00713};
DE AltName: Full=Glycine cleavage system P-protein subunit 2 {ECO:0000255|HAMAP-Rule:MF_00713};
DE AltName: Full=Glycine decarboxylase subunit 2 {ECO:0000255|HAMAP-Rule:MF_00713};
DE AltName: Full=Glycine dehydrogenase (aminomethyl-transferring) subunit 2 {ECO:0000255|HAMAP-Rule:MF_00713};
GN Name=gcvPB {ECO:0000255|HAMAP-Rule:MF_00713}; OrderedLocusNames=TTHA0526;
OS Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8).
OC Bacteria; Deinococcus-Thermus; Deinococci; Thermales; Thermaceae; Thermus.
OX NCBI_TaxID=300852;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 27634 / DSM 579 / HB8;
RA Masui R., Kurokawa K., Nakagawa N., Tokunaga F., Koyama Y., Shibata T.,
RA Oshima T., Yokoyama S., Yasunaga T., Kuramitsu S.;
RT "Complete genome sequence of Thermus thermophilus HB8.";
RL Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).
RX PubMed=15791207; DOI=10.1038/sj.emboj.7600632;
RA Nakai T., Nakagawa N., Maoka N., Masui R., Kuramitsu S., Kamiya N.;
RT "Structure of P-protein of the glycine cleavage system: implications for
RT nonketotic hyperglycinemia.";
RL EMBO J. 24:1523-1536(2005).
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:0000255|HAMAP-Rule:MF_00713}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(R)-N(6)-lipoyl-L-lysyl-[glycine-cleavage complex H protein] +
CC glycine + H(+) = (R)-N(6)-(S(8)-aminomethyldihydrolipoyl)-L-lysyl-
CC [glycine-cleavage complex H protein] + CO2; 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; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_00713};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00713};
CC -!- SUBUNIT: The glycine cleavage system is composed of four proteins: P,
CC T, L and H. In this organism, the P 'protein' is a heterodimer of two
CC subunits. {ECO:0000255|HAMAP-Rule:MF_00713}.
CC -!- SIMILARITY: Belongs to the GcvP family. C-terminal subunit subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_00713}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AP008226; BAD70349.1; -; Genomic_DNA.
DR RefSeq; WP_011228003.1; NC_006461.1.
DR RefSeq; YP_143792.1; NC_006461.1.
DR PDB; 1WYT; X-ray; 2.40 A; B/D=1-474.
DR PDB; 1WYU; X-ray; 2.10 A; B/D/F/H=1-474.
DR PDB; 1WYV; X-ray; 2.40 A; B/D/F/H=1-474.
DR PDBsum; 1WYT; -.
DR PDBsum; 1WYU; -.
DR PDBsum; 1WYV; -.
DR AlphaFoldDB; Q5SKW7; -.
DR SMR; Q5SKW7; -.
DR STRING; 300852.55771908; -.
DR PRIDE; Q5SKW7; -.
DR EnsemblBacteria; BAD70349; BAD70349; BAD70349.
DR GeneID; 3168946; -.
DR KEGG; ttj:TTHA0526; -.
DR PATRIC; fig|300852.9.peg.524; -.
DR eggNOG; COG1003; Bacteria.
DR HOGENOM; CLU_004620_5_0_0; -.
DR OMA; MHINLHK; -.
DR PhylomeDB; Q5SKW7; -.
DR EvolutionaryTrace; Q5SKW7; -.
DR Proteomes; UP000000532; Chromosome.
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; 1.
DR Gene3D; 3.40.640.10; -; 1.
DR Gene3D; 3.90.1150.10; -; 1.
DR HAMAP; MF_00713; GcvPB; 1.
DR InterPro; IPR023012; GcvPB.
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 PANTHER; PTHR11773; PTHR11773; 1.
DR Pfam; PF02347; GDC-P; 1.
DR SUPFAM; SSF53383; SSF53383; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Oxidoreductase; Pyridoxal phosphate; Reference proteome.
FT CHAIN 1..474
FT /note="Probable glycine dehydrogenase (decarboxylating)
FT subunit 2"
FT /id="PRO_1000045709"
FT MOD_RES 266
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00713"
FT HELIX 6..9
FT /evidence="ECO:0007829|PDB:1WYU"
FT HELIX 26..29
FT /evidence="ECO:0007829|PDB:1WYU"
FT HELIX 32..34
FT /evidence="ECO:0007829|PDB:1WYU"
FT HELIX 47..58
FT /evidence="ECO:0007829|PDB:1WYU"
FT TURN 64..66
FT /evidence="ECO:0007829|PDB:1WYU"
FT TURN 72..74
FT /evidence="ECO:0007829|PDB:1WYU"
FT HELIX 81..88
FT /evidence="ECO:0007829|PDB:1WYU"
FT HELIX 99..101
FT /evidence="ECO:0007829|PDB:1WYU"
FT HELIX 103..120
FT /evidence="ECO:0007829|PDB:1WYU"
FT STRAND 123..126
FT /evidence="ECO:0007829|PDB:1WYU"
FT HELIX 132..149
FT /evidence="ECO:0007829|PDB:1WYU"
FT TURN 153..155
FT /evidence="ECO:0007829|PDB:1WYU"
FT STRAND 158..162
FT /evidence="ECO:0007829|PDB:1WYU"
FT HELIX 168..175
FT /evidence="ECO:0007829|PDB:1WYU"
FT STRAND 179..183
FT /evidence="ECO:0007829|PDB:1WYU"
FT STRAND 189..191
FT /evidence="ECO:0007829|PDB:1WYU"
FT HELIX 193..199
FT /evidence="ECO:0007829|PDB:1WYU"
FT STRAND 204..209
FT /evidence="ECO:0007829|PDB:1WYU"
FT HELIX 222..231
FT /evidence="ECO:0007829|PDB:1WYU"
FT STRAND 235..239
FT /evidence="ECO:0007829|PDB:1WYU"
FT HELIX 240..245
FT /evidence="ECO:0007829|PDB:1WYU"
FT TURN 246..249
FT /evidence="ECO:0007829|PDB:1WYU"
FT HELIX 252..255
FT /evidence="ECO:0007829|PDB:1WYU"
FT STRAND 258..261
FT /evidence="ECO:0007829|PDB:1WYU"
FT TURN 264..268
FT /evidence="ECO:0007829|PDB:1WYU"
FT HELIX 273..275
FT /evidence="ECO:0007829|PDB:1WYT"
FT STRAND 282..284
FT /evidence="ECO:0007829|PDB:1WYU"
FT HELIX 286..291
FT /evidence="ECO:0007829|PDB:1WYU"
FT STRAND 296..299
FT /evidence="ECO:0007829|PDB:1WYU"
FT STRAND 304..307
FT /evidence="ECO:0007829|PDB:1WYU"
FT STRAND 317..319
FT /evidence="ECO:0007829|PDB:1WYU"
FT HELIX 324..362
FT /evidence="ECO:0007829|PDB:1WYU"
FT STRAND 377..380
FT /evidence="ECO:0007829|PDB:1WYU"
FT HELIX 387..396
FT /evidence="ECO:0007829|PDB:1WYU"
FT STRAND 403..405
FT /evidence="ECO:0007829|PDB:1WYU"
FT STRAND 414..416
FT /evidence="ECO:0007829|PDB:1WYU"
FT HELIX 424..438
FT /evidence="ECO:0007829|PDB:1WYU"
FT HELIX 442..446
FT /evidence="ECO:0007829|PDB:1WYU"
FT STRAND 451..454
FT /evidence="ECO:0007829|PDB:1WYU"
FT HELIX 459..464
FT /evidence="ECO:0007829|PDB:1WYU"
FT STRAND 469..471
FT /evidence="ECO:0007829|PDB:1WYU"
SQ SEQUENCE 474 AA; 52709 MW; A8B48175AF156C1D CRC64;
MSFPLIFERS RKGRRGLKLV KAVPKAEDLI PKEHLREVPP RLPEVDELTL VRHYTGLSRR
QVGVDTTFYP LGSCTMKYNP KLHEEAARLF ADLHPYQDPR TAQGALRLMW ELGEYLKALT
GMDAITLEPA AGAHGELTGI LIIRAYHEDR GEGRTRRVVL VPDSAHGSNP ATASMAGYQV
REIPSGPEGE VDLEALKREL GPHVAALMLT NPNTLGLFER RILEISRLCK EAGVQLYYDG
ANLNAIMGWA RPGDMGFDVV HLNLHKTFTV PHGGGGPGSG PVGVKAHLAP YLPVPLVERG
EEGFYLDFDR PKSIGRVRSF YGNFLALVRA WAYIRTLGLE GLKKAAALAV LNARYLKELL
KEKGYRVPYD GPSMHEFVAQ PPEGFRALDL AKGLLELGFH PPTVYFPLIV KEALMVEPTE
TEAKETLEAF AEAMGALLKK PKEWLENAPY STPVRRLDEL RANKHPKLTY FDEG
