ID U2YMB8_9SPHN Unreviewed; 430 AA.
AC U2YMB8;
DT 13-NOV-2013, integrated into UniProtKB/TrEMBL.
DT 13-NOV-2013, sequence version 1.
DT 27-MAR-2024, entry version 50.
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:GAD49855.1};
GN ORFNames=NT2_06_02950 {ECO:0000313|EMBL:GAD49855.1};
OS Caenibius tardaugens NBRC 16725.
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales;
OC Erythrobacteraceae; Caenibius.
OX NCBI_TaxID=1219035 {ECO:0000313|EMBL:GAD49855.1, ECO:0000313|Proteomes:UP000016568};
RN [1] {ECO:0000313|EMBL:GAD49855.1, ECO:0000313|Proteomes:UP000016568}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=NBRC 16725 {ECO:0000313|EMBL:GAD49855.1,
RC ECO:0000313|Proteomes:UP000016568};
RA Isaki S., Hosoyama A., Tsuchikane K., Katsumata H., Ando Y., Yamazaki S.,
RA Fujita N.;
RT "Whole genome shotgun sequence of Novosphingobium tardaugens NBRC 16725.";
RL Submitted (SEP-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|ARBA:ARBA00011738, ECO:0000256|HAMAP-
CC 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}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:GAD49855.1}.
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DR EMBL; BASZ01000006; GAD49855.1; -; Genomic_DNA.
DR RefSeq; WP_021690760.1; NZ_CP034179.1.
DR AlphaFoldDB; U2YMB8; -.
DR KEGG; ntd:EGO55_17915; -.
DR eggNOG; COG0112; Bacteria.
DR OrthoDB; 9803846at2; -.
DR UniPathway; UPA00193; -.
DR UniPathway; UPA00288; UER01023.
DR Proteomes; UP000016568; Unassembled WGS sequence.
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:SF28; 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|HAMAP-Rule:MF_00051};
KW Cytoplasm {ECO:0000256|ARBA:ARBA00022490, ECO:0000256|HAMAP-Rule:MF_00051};
KW Methyltransferase {ECO:0000313|EMBL:GAD49855.1};
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}; Reference proteome {ECO:0000313|Proteomes:UP000016568};
KW Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000256|HAMAP-
KW Rule:MF_00051}.
FT DOMAIN 14..391
FT /note="Serine hydroxymethyltransferase-like"
FT /evidence="ECO:0000259|Pfam:PF00464"
FT BINDING 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 131..133
FT /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57453"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00051"
FT BINDING 251
FT /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57453"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00051"
FT BINDING 360..362
FT /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57453"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00051"
FT SITE 235
FT /note="Plays an important role in substrate specificity"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00051"
FT MOD_RES 236
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00051,
FT ECO:0000256|PIRSR:PIRSR000412-50"
SQ SEQUENCE 430 AA; 46407 MW; D2B398E2E51A348E CRC64;
MSTDTMNRFW NDTLAQADPE VAAAIASELK RQRNKIELIA SENIASKAVL EATGSVFTNK
YAEGYPGKRY YGGCDYADVV ETLAIERAKQ LFGCAFANVQ PNSGSQMNQA VFLALLQPGD
TFMGLDLNSG GHLTHGSPVN MSGKWFNPVP YGVRPDDELI DMDEVARIAR ECKPKLIIAG
GTAYSRIWDF PRFREIADEV GAYLMVDMSH FSGLVAGGEH PSPFPHAHVV TSTTHKSLRG
PRSGIILTND EDLAKKFNSA VFPGLQGGPL VHVIAAKAVA FGEALRPDFK VYAKNVVANA
RALAASVEEH GLRIVSGGTD NHLMLVDLTA KDVTGKSAEK GLDRAWLTCN KNGIPFDTRS
PFVTSGVRLG TPAGTTRGFG TDEFRKIGAL IAEVVEGLSR NGEEGDGQVE ERVRAQVEEL
CQSFPVYPGM
//
