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GLYA2_VIBPA
ID   GLYA2_VIBPA             Reviewed;         431 AA.
AC   Q87I03;
DT   23-MAY-2003, integrated into UniProtKB/Swiss-Prot.
DT   23-MAY-2003, sequence version 1.
DT   03-AUG-2022, entry version 113.
DE   RecName: Full=Serine hydroxymethyltransferase 2 {ECO:0000255|HAMAP-Rule:MF_00051};
DE            Short=SHMT 2 {ECO:0000255|HAMAP-Rule:MF_00051};
DE            Short=Serine methylase 2 {ECO:0000255|HAMAP-Rule:MF_00051};
DE            EC=2.1.2.1 {ECO:0000255|HAMAP-Rule:MF_00051};
GN   Name=glyA2 {ECO:0000255|HAMAP-Rule:MF_00051}; OrderedLocusNames=VPA0803;
OS   Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC   Vibrio.
OX   NCBI_TaxID=223926;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=RIMD 2210633;
RX   PubMed=12620739; DOI=10.1016/s0140-6736(03)12659-1;
RA   Makino K., Oshima K., Kurokawa K., Yokoyama K., Uda T., Tagomori K.,
RA   Iijima Y., Najima M., Nakano M., Yamashita A., Kubota Y., Kimura S.,
RA   Yasunaga T., Honda T., Shinagawa H., Hattori M., Iida T.;
RT   "Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism
RT   distinct from that of V. cholerae.";
RL   Lancet 361:743-749(2003).
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:0000255|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:0000255|HAMAP-Rule:MF_00051};
CC   -!- COFACTOR:
CC       Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_00051};
CC   -!- PATHWAY: One-carbon metabolism; tetrahydrofolate interconversion.
CC       {ECO:0000255|HAMAP-Rule:MF_00051}.
CC   -!- PATHWAY: Amino-acid biosynthesis; glycine biosynthesis; glycine from L-
CC       serine: step 1/1. {ECO:0000255|HAMAP-Rule:MF_00051}.
CC   -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_00051}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00051}.
CC   -!- SIMILARITY: Belongs to the SHMT family. {ECO:0000255|HAMAP-
CC       Rule:MF_00051}.
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DR   EMBL; BA000032; BAC62146.1; -; Genomic_DNA.
DR   RefSeq; NP_800313.1; NC_004605.1.
DR   RefSeq; WP_005478453.1; NC_004605.1.
DR   AlphaFoldDB; Q87I03; -.
DR   SMR; Q87I03; -.
DR   STRING; 223926.28809038; -.
DR   EnsemblBacteria; BAC62146; BAC62146; BAC62146.
DR   GeneID; 1191492; -.
DR   KEGG; vpa:VPA0803; -.
DR   PATRIC; fig|223926.6.peg.3734; -.
DR   eggNOG; COG0112; Bacteria.
DR   HOGENOM; CLU_022477_2_1_6; -.
DR   OMA; RCQHSEV; -.
DR   UniPathway; UPA00193; -.
DR   UniPathway; UPA00288; UER01023.
DR   Proteomes; UP000002493; Chromosome 2.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0004372; F:glycine hydroxymethyltransferase activity; IEA:UniProtKB-UniRule.
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:0035999; P:tetrahydrofolate interconversion; IEA:UniProtKB-UniPathway.
DR   CDD; cd00378; SHMT; 1.
DR   Gene3D; 3.40.640.10; -; 1.
DR   Gene3D; 3.90.1150.10; -; 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; PTHR11680; 1.
DR   Pfam; PF00464; SHMT; 1.
DR   PIRSF; PIRSF000412; SHMT; 1.
DR   SUPFAM; SSF53383; SSF53383; 1.
DR   PROSITE; PS00096; SHMT; 1.
PE   3: Inferred from homology;
KW   Amino-acid biosynthesis; Cytoplasm; One-carbon metabolism;
KW   Pyridoxal phosphate; Reference proteome; Transferase.
FT   CHAIN           1..431
FT                   /note="Serine hydroxymethyltransferase 2"
FT                   /id="PRO_0000113693"
FT   BINDING         131
FT                   /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT                   /ligand_id="ChEBI:CHEBI:57453"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00051"
FT   BINDING         135..137
FT                   /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT                   /ligand_id="ChEBI:CHEBI:57453"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00051"
FT   SITE            239
FT                   /note="Plays an important role in substrate specificity"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00051"
FT   MOD_RES         240
FT                   /note="N6-(pyridoxal phosphate)lysine"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00051"
SQ   SEQUENCE   431 AA;  46507 MW;  CC0A30799E80C6E7 CRC64;
     MNKSYPNHSL ENFFSTNLSA TDDAVFAGIQ AEFTRQNEQI ELIASENIVS KAVMQAQGTC
     LTNKYAEGYP GRRYYGGCEH VDTVEAIAIE RAKKLFNCEY ANVQPHSGAQ ANGAVKLALL
     QPGDTILGMS LDAGGHLTHG ARPALSGKWF NAVQYGVDRE TLEINYDDVR ALALEHKPKM
     IIAGGSAIPR TIDFAKFREI ADEVNAILMV DMAHIAGLIA TGAHPSPLPH AHVVTTTTHK
     TLRGPRGGMI LTNHEDIIKK INSAVFPGLQ GGPLMHVIAA KAVAFGEALG PEFKTYIDSV
     INNAKVLAEV LQTRGCDIVT GGTDTHLMLV DLRPKGLKGN KAEEALERAG ITCNKNGIPF
     DTEKPMITSG IRLGTPAGTS RGFGAEEFKL IGNWIGDVLD GLVNNPEGDA IVEKRVRKEV
     KELCSRFPLY Q
 
 
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