GLYA_STAAC
ID GLYA_STAAC Reviewed; 412 AA.
AC Q5HE87;
DT 19-JUL-2005, integrated into UniProtKB/Swiss-Prot.
DT 15-FEB-2005, sequence version 1.
DT 03-AUG-2022, entry version 108.
DE RecName: Full=Serine hydroxymethyltransferase {ECO:0000255|HAMAP-Rule:MF_00051};
DE Short=SHMT {ECO:0000255|HAMAP-Rule:MF_00051};
DE Short=Serine methylase {ECO:0000255|HAMAP-Rule:MF_00051};
DE EC=2.1.2.1 {ECO:0000255|HAMAP-Rule:MF_00051};
GN Name=glyA {ECO:0000255|HAMAP-Rule:MF_00051}; OrderedLocusNames=SACOL2105;
OS Staphylococcus aureus (strain COL).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae;
OC Staphylococcus.
OX NCBI_TaxID=93062;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=COL;
RX PubMed=15774886; DOI=10.1128/jb.187.7.2426-2438.2005;
RA Gill S.R., Fouts D.E., Archer G.L., Mongodin E.F., DeBoy R.T., Ravel J.,
RA Paulsen I.T., Kolonay J.F., Brinkac L.M., Beanan M.J., Dodson R.J.,
RA Daugherty S.C., Madupu R., Angiuoli S.V., Durkin A.S., Haft D.H.,
RA Vamathevan J.J., Khouri H., Utterback T.R., Lee C., Dimitrov G., Jiang L.,
RA Qin H., Weidman J., Tran K., Kang K.H., Hance I.R., Nelson K.E.,
RA Fraser C.M.;
RT "Insights on evolution of virulence and resistance from the complete genome
RT analysis of an early methicillin-resistant Staphylococcus aureus strain and
RT a biofilm-producing methicillin-resistant Staphylococcus epidermidis
RT strain.";
RL J. Bacteriol. 187:2426-2438(2005).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.92 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS,
RP AND SUBUNIT.
RG Center for structural genomics of infectious diseases (CSGID);
RA Osipiuk J., Makowska-Grzyska M., Kwon K., Anderson W.F., Joachimiak A.;
RT "Serine hydroxymethyltransferase from Staphylococcus aureus S95P mutant.";
RL Submitted (NOV-2010) to the PDB data bank.
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 ECO:0000269|Ref.2}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00051}.
CC -!- SIMILARITY: Belongs to the SHMT family. {ECO:0000255|HAMAP-
CC Rule:MF_00051, ECO:0000305}.
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DR EMBL; CP000046; AAW38415.1; -; Genomic_DNA.
DR RefSeq; WP_000120494.1; NC_002951.2.
DR PDB; 3PGY; X-ray; 1.92 A; A/B/C/D=1-412.
DR PDBsum; 3PGY; -.
DR AlphaFoldDB; Q5HE87; -.
DR SMR; Q5HE87; -.
DR PRIDE; Q5HE87; -.
DR EnsemblBacteria; AAW38415; AAW38415; SACOL2105.
DR KEGG; sac:SACOL2105; -.
DR HOGENOM; CLU_022477_2_1_9; -.
DR OMA; SHPAGLI; -.
DR BRENDA; 2.1.2.1; 3352.
DR UniPathway; UPA00193; -.
DR UniPathway; UPA00288; UER01023.
DR EvolutionaryTrace; Q5HE87; -.
DR Proteomes; UP000000530; Chromosome.
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 1: Evidence at protein level;
KW 3D-structure; Amino-acid biosynthesis; Cytoplasm; One-carbon metabolism;
KW Pyridoxal phosphate; Transferase.
FT CHAIN 1..412
FT /note="Serine hydroxymethyltransferase"
FT /id="PRO_0000113661"
FT BINDING 117
FT /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57453"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00051"
FT BINDING 121..123
FT /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57453"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00051"
FT SITE 225
FT /note="Plays an important role in substrate specificity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00051"
FT MOD_RES 226
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00051"
FT HELIX 2..7
FT /evidence="ECO:0007829|PDB:3PGY"
FT HELIX 9..24
FT /evidence="ECO:0007829|PDB:3PGY"
FT STRAND 25..27
FT /evidence="ECO:0007829|PDB:3PGY"
FT HELIX 37..43
FT /evidence="ECO:0007829|PDB:3PGY"
FT HELIX 46..49
FT /evidence="ECO:0007829|PDB:3PGY"
FT HELIX 65..82
FT /evidence="ECO:0007829|PDB:3PGY"
FT STRAND 85..88
FT /evidence="ECO:0007829|PDB:3PGY"
FT HELIX 94..105
FT /evidence="ECO:0007829|PDB:3PGY"
FT STRAND 111..115
FT /evidence="ECO:0007829|PDB:3PGY"
FT HELIX 131..134
FT /evidence="ECO:0007829|PDB:3PGY"
FT STRAND 135..140
FT /evidence="ECO:0007829|PDB:3PGY"
FT TURN 145..147
FT /evidence="ECO:0007829|PDB:3PGY"
FT HELIX 152..162
FT /evidence="ECO:0007829|PDB:3PGY"
FT STRAND 165..170
FT /evidence="ECO:0007829|PDB:3PGY"
FT HELIX 180..190
FT /evidence="ECO:0007829|PDB:3PGY"
FT STRAND 193..197
FT /evidence="ECO:0007829|PDB:3PGY"
FT TURN 199..201
FT /evidence="ECO:0007829|PDB:3PGY"
FT HELIX 202..206
FT /evidence="ECO:0007829|PDB:3PGY"
FT HELIX 213..215
FT /evidence="ECO:0007829|PDB:3PGY"
FT STRAND 218..226
FT /evidence="ECO:0007829|PDB:3PGY"
FT STRAND 234..238
FT /evidence="ECO:0007829|PDB:3PGY"
FT HELIX 240..242
FT /evidence="ECO:0007829|PDB:3PGY"
FT HELIX 243..250
FT /evidence="ECO:0007829|PDB:3PGY"
FT TURN 251..254
FT /evidence="ECO:0007829|PDB:3PGY"
FT HELIX 260..274
FT /evidence="ECO:0007829|PDB:3PGY"
FT HELIX 276..298
FT /evidence="ECO:0007829|PDB:3PGY"
FT HELIX 304..306
FT /evidence="ECO:0007829|PDB:3PGY"
FT STRAND 309..316
FT /evidence="ECO:0007829|PDB:3PGY"
FT HELIX 317..321
FT /evidence="ECO:0007829|PDB:3PGY"
FT HELIX 325..334
FT /evidence="ECO:0007829|PDB:3PGY"
FT STRAND 340..342
FT /evidence="ECO:0007829|PDB:3PGY"
FT TURN 351..353
FT /evidence="ECO:0007829|PDB:3PGY"
FT STRAND 355..360
FT /evidence="ECO:0007829|PDB:3PGY"
FT HELIX 362..366
FT /evidence="ECO:0007829|PDB:3PGY"
FT HELIX 371..386
FT /evidence="ECO:0007829|PDB:3PGY"
FT TURN 387..389
FT /evidence="ECO:0007829|PDB:3PGY"
FT HELIX 391..407
FT /evidence="ECO:0007829|PDB:3PGY"
SQ SEQUENCE 412 AA; 45172 MW; CF7DD04B38CBAC56 CRC64;
MSYITKQDKV IAEAIEREFQ RQNSNIELIA SENFVSEAVM EAQGSVLTNK YAEGYPGRRY
YGGCEFVDVT ESIAIDRAKA LFGAEHVNVQ PHSGSQANMA VYLVALEMGD TVLGMNLSHG
GHLTHGAPVN FSGKFYNFVE YGVDKDTERI NYDEVRKLAL EHKPKLIVAG ASAYSRTIDF
KKFKEIADEV NAKLMVDMAH IAGLVAAGLH PNPVEYADFV TTTTHKTLRG PRGGMILCKE
EYKKDIDKTI FPGIQGGPLE HVIAAKAVAF GEALENNFKT YQQQVVKNAK VLAEALINEG
FRIVSGGTDN HLVAVDVKGS IGLTGKEAEE TLDSVGITCN KNTIPFDQEK PFVTSGIRLG
TPAATTRGFD EKAFEEVAKI ISLALKNSKD EEKLQQAKER VAKLTAEYPL YQ
