ID A0A068QV04_9GAMM Unreviewed; 417 AA.
AC A0A068QV04;
DT 01-OCT-2014, integrated into UniProtKB/TrEMBL.
DT 01-OCT-2014, sequence version 1.
DT 24-JAN-2024, entry version 46.
DE RecName: Full=Serine hydroxymethyltransferase {ECO:0000256|HAMAP-Rule:MF_00051};
DE Short=SHMT {ECO:0000256|HAMAP-Rule:MF_00051};
DE Short=Serine methylase {ECO:0000256|HAMAP-Rule:MF_00051};
DE EC=2.1.2.1 {ECO:0000256|HAMAP-Rule:MF_00051};
GN Name=glyA {ECO:0000256|HAMAP-Rule:MF_00051,
GN ECO:0000313|EMBL:CDG18491.1};
GN ORFNames=XDD1_2792 {ECO:0000313|EMBL:CDG18491.1};
OS Xenorhabdus doucetiae.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC Morganellaceae; Xenorhabdus.
OX NCBI_TaxID=351671 {ECO:0000313|EMBL:CDG18491.1, ECO:0000313|Proteomes:UP000032721};
RN [1] {ECO:0000313|EMBL:CDG18491.1, ECO:0000313|Proteomes:UP000032721}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=FRM16 / DSM 17909 {ECO:0000313|Proteomes:UP000032721};
RA Genoscope - CEA;
RL Submitted (JUL-2013) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Catalyzes the reversible interconversion of serine and
CC glycine with tetrahydrofolate (THF) serving as the one-carbon carrier.
CC This reaction serves as the major source of one-carbon groups required
CC for the biosynthesis of purines, thymidylate, methionine, and other
CC important biomolecules. Also exhibits THF-independent aldolase activity
CC toward beta-hydroxyamino acids, producing glycine and aldehydes, via a
CC retro-aldol mechanism. {ECO:0000256|HAMAP-Rule:MF_00051}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + glycine + H2O =
CC (6S)-5,6,7,8-tetrahydrofolate + L-serine; Xref=Rhea:RHEA:15481,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15636, ChEBI:CHEBI:33384,
CC ChEBI:CHEBI:57305, ChEBI:CHEBI:57453; EC=2.1.2.1;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_00051};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000256|ARBA:ARBA00001933,
CC ECO:0000256|HAMAP-Rule:MF_00051, ECO:0000256|PIRSR:PIRSR000412-50};
CC -!- PATHWAY: Amino-acid biosynthesis; glycine biosynthesis; glycine from L-
CC serine: step 1/1. {ECO:0000256|HAMAP-Rule:MF_00051}.
CC -!- PATHWAY: One-carbon metabolism; tetrahydrofolate interconversion.
CC {ECO:0000256|HAMAP-Rule:MF_00051}.
CC -!- SUBUNIT: Homodimer. {ECO:0000256|HAMAP-Rule:MF_00051}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00051}.
CC -!- SIMILARITY: Belongs to the SHMT family. {ECO:0000256|ARBA:ARBA00006376,
CC ECO:0000256|HAMAP-Rule:MF_00051}.
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DR EMBL; FO704550; CDG18491.1; -; Genomic_DNA.
DR RefSeq; WP_045971759.1; NZ_VNHN01000015.1.
DR AlphaFoldDB; A0A068QV04; -.
DR STRING; 351671.XDD1_2792; -.
DR KEGG; xdo:XDD1_2792; -.
DR HOGENOM; CLU_022477_2_1_6; -.
DR OrthoDB; 9803846at2; -.
DR UniPathway; UPA00193; -.
DR UniPathway; UPA00288; UER01023.
DR Proteomes; UP000032721; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0004372; F:glycine hydroxymethyltransferase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0008168; F:methyltransferase activity; IEA:UniProtKB-KW.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IEA:UniProtKB-UniRule.
DR GO; GO:0019264; P:glycine biosynthetic process from serine; IEA:UniProtKB-UniRule.
DR GO; GO:0032259; P:methylation; IEA:UniProtKB-KW.
DR GO; GO:0035999; P:tetrahydrofolate interconversion; IEA:UniProtKB-UniPathway.
DR CDD; cd00378; SHMT; 1.
DR Gene3D; 3.90.1150.10; Aspartate Aminotransferase, domain 1; 1.
DR Gene3D; 3.40.640.10; Type I PLP-dependent aspartate aminotransferase-like (Major domain); 1.
DR HAMAP; MF_00051; SHMT; 1.
DR InterPro; IPR015424; PyrdxlP-dep_Trfase.
DR InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
DR InterPro; IPR015422; PyrdxlP-dep_Trfase_small.
DR InterPro; IPR001085; Ser_HO-MeTrfase.
DR InterPro; IPR019798; Ser_HO-MeTrfase_PLP_BS.
DR InterPro; IPR039429; SHMT-like_dom.
DR PANTHER; PTHR11680; SERINE HYDROXYMETHYLTRANSFERASE; 1.
DR PANTHER; PTHR11680:SF50; SERINE HYDROXYMETHYLTRANSFERASE; 1.
DR Pfam; PF00464; SHMT; 1.
DR PIRSF; PIRSF000412; SHMT; 1.
DR SUPFAM; SSF53383; PLP-dependent transferases; 1.
DR PROSITE; PS00096; SHMT; 1.
PE 3: Inferred from homology;
KW Amino-acid biosynthesis {ECO:0000256|ARBA:ARBA00022605, ECO:0000256|HAMAP-
KW Rule:MF_00051};
KW Cytoplasm {ECO:0000256|ARBA:ARBA00022490, ECO:0000256|HAMAP-Rule:MF_00051};
KW Methyltransferase {ECO:0000313|EMBL:CDG18491.1};
KW One-carbon metabolism {ECO:0000256|ARBA:ARBA00022563, ECO:0000256|HAMAP-
KW Rule:MF_00051};
KW Pyridoxal phosphate {ECO:0000256|ARBA:ARBA00022898, ECO:0000256|HAMAP-
KW Rule:MF_00051};
KW Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000256|HAMAP-
KW Rule:MF_00051}.
FT DOMAIN 9..385
FT /note="Serine hydroxymethyltransferase-like"
FT /evidence="ECO:0000259|Pfam:PF00464"
FT BINDING 121
FT /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57453"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00051"
FT BINDING 125..127
FT /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57453"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00051"
FT BINDING 246
FT /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57453"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00051"
FT BINDING 355..357
FT /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57453"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00051"
FT SITE 228
FT /note="Plays an important role in substrate specificity"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00051"
FT MOD_RES 229
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00051,
FT ECO:0000256|PIRSR:PIRSR000412-50"
SQ SEQUENCE 417 AA; 45595 MW; FA8595074B2A6FAD CRC64;
MLKREMNIAN YDPELWQAME QEVCRQEEHI ELIASENYTS PRVMQAQGSQ LTNKYAEGYP
GKRYYGGCEY VDIVEQLAID RAKELFGADY ANVQPHSGSQ ANAAVYMTLL KPGDTVLGMN
LAHGGHLTHG SPVNFSGKLY NIVPYGIDEA GKIDYDDIRA QAQKHQPKMI IGGFSAYSGI
VDWAKMREIA DEIGAYLFVD MAHVAGLVAA GVYPNPVPHA HVVTTTTHKT LAGPRGGLIL
AKGGDEEFYK KLNSSVFPGS QGGPLMHVIA GKAVALKEAM EPEFKAYQHQ VAKNAKAMVD
VFLQRGYKVV SGETENHLFL LDLVDKNITG KEADAALGRA NITVNKNSVP NDPRSPFVTS
GIRIGTPAIT RRGFKEAETC ELAGWMCDVL DNINDEATIE SVKQKVLNIC AKYPVYA
//