GLYA_SALTY
ID GLYA_SALTY Reviewed; 417 AA.
AC P0A2E1; P06192;
DT 01-JAN-1988, integrated into UniProtKB/Swiss-Prot.
DT 15-MAR-2005, sequence version 1.
DT 03-AUG-2022, entry version 106.
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=STM2555;
OS Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Salmonella.
OX NCBI_TaxID=99287;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=LT2;
RX PubMed=2134182; DOI=10.3109/10425179009016038;
RA Steiert J.G., Urbanowski M.L., Stauffer L.T., Plamann M.D., Stauffer G.V.;
RT "Nucleotide sequence of the Salmonella typhimurium glyA gene.";
RL DNA Seq. 1:107-113(1990).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LT2 / SGSC1412 / ATCC 700720;
RX PubMed=11677609; DOI=10.1038/35101614;
RA McClelland M., Sanderson K.E., Spieth J., Clifton S.W., Latreille P.,
RA Courtney L., Porwollik S., Ali J., Dante M., Du F., Hou S., Layman D.,
RA Leonard S., Nguyen C., Scott K., Holmes A., Grewal N., Mulvaney E.,
RA Ryan E., Sun H., Florea L., Miller W., Stoneking T., Nhan M., Waterston R.,
RA Wilson R.K.;
RT "Complete genome sequence of Salmonella enterica serovar Typhimurium LT2.";
RL Nature 413:852-856(2001).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 179-215.
RC STRAIN=LT2;
RX PubMed=6325301; DOI=10.1016/0378-1119(84)90237-3;
RA Urbanowski M.L., Plamann M.D., Stauffer L.T., Stauffer G.V.;
RT "Cloning and characterization of the gene for Salmonella typhimurium serine
RT hydroxymethyltransferase.";
RL Gene 27:47-54(1984).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS), AND SUBUNIT.
RG Center for structural genomics of infectious diseases (CSGID);
RA Osipiuk J., Nocek B., Zhou M., Stam J., Anderson W.F., Joachimiak A.;
RT "X-ray crystal structure of serine hydroxymethyltransferase from Salmonella
RT typhimurium.";
RL Submitted (FEB-2009) 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.4}.
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; X15816; CAA33808.1; -; Genomic_DNA.
DR EMBL; AE006468; AAL21449.1; -; Genomic_DNA.
DR EMBL; K01616; AAA27135.1; -; Genomic_DNA.
DR PIR; B48427; B48427.
DR RefSeq; NP_461490.1; NC_003197.2.
DR RefSeq; WP_000919178.1; NC_003197.2.
DR PDB; 3GBX; X-ray; 1.80 A; A/B=1-417.
DR PDBsum; 3GBX; -.
DR AlphaFoldDB; P0A2E1; -.
DR SMR; P0A2E1; -.
DR STRING; 99287.STM2555; -.
DR PaxDb; P0A2E1; -.
DR EnsemblBacteria; AAL21449; AAL21449; STM2555.
DR GeneID; 1254077; -.
DR KEGG; stm:STM2555; -.
DR PATRIC; fig|99287.12.peg.2695; -.
DR HOGENOM; CLU_022477_2_1_6; -.
DR OMA; SHPAGLI; -.
DR PhylomeDB; P0A2E1; -.
DR BioCyc; SENT99287:STM2555-MON; -.
DR BRENDA; 2.1.2.1; 5542.
DR UniPathway; UPA00193; -.
DR UniPathway; UPA00288; UER01023.
DR EvolutionaryTrace; P0A2E1; -.
DR Proteomes; UP000001014; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0004372; F:glycine hydroxymethyltransferase activity; IBA:GO_Central.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IBA:GO_Central.
DR GO; GO:0070905; F:serine binding; IBA:GO_Central.
DR GO; GO:0008270; F:zinc ion binding; IBA:GO_Central.
DR GO; GO:0046655; P:folic acid metabolic process; IBA:GO_Central.
DR GO; GO:0019264; P:glycine biosynthetic process from serine; IBA:GO_Central.
DR GO; GO:0006565; P:L-serine catabolic process; IBA:GO_Central.
DR GO; GO:0006730; P:one-carbon metabolic process; IBA:GO_Central.
DR GO; GO:0035999; P:tetrahydrofolate interconversion; IEA:UniProtKB-UniPathway.
DR GO; GO:0046653; P:tetrahydrofolate metabolic process; IBA:GO_Central.
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; Reference proteome; Transferase.
FT CHAIN 1..417
FT /note="Serine hydroxymethyltransferase"
FT /id="PRO_0000113658"
FT BINDING 121
FT /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57453"
FT /evidence="ECO:0000255|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:0000255|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:0000255|HAMAP-Rule:MF_00051"
FT SITE 228
FT /note="Plays an important role in substrate specificity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00051"
FT MOD_RES 229
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00051"
FT CONFLICT 161
FT /note="L -> S (in Ref. 1; CAA33808)"
FT /evidence="ECO:0000305"
FT CONFLICT 193
FT /note="I -> Y (in Ref. 3; AAA27135)"
FT /evidence="ECO:0000305"
FT CONFLICT 275
FT /note="A -> G (in Ref. 1; CAA33808)"
FT /evidence="ECO:0000305"
FT TURN 3..5
FT /evidence="ECO:0007829|PDB:3GBX"
FT HELIX 8..11
FT /evidence="ECO:0007829|PDB:3GBX"
FT HELIX 13..28
FT /evidence="ECO:0007829|PDB:3GBX"
FT STRAND 29..31
FT /evidence="ECO:0007829|PDB:3GBX"
FT HELIX 41..47
FT /evidence="ECO:0007829|PDB:3GBX"
FT HELIX 50..53
FT /evidence="ECO:0007829|PDB:3GBX"
FT HELIX 72..86
FT /evidence="ECO:0007829|PDB:3GBX"
FT STRAND 89..92
FT /evidence="ECO:0007829|PDB:3GBX"
FT HELIX 98..109
FT /evidence="ECO:0007829|PDB:3GBX"
FT STRAND 115..121
FT /evidence="ECO:0007829|PDB:3GBX"
FT HELIX 136..139
FT /evidence="ECO:0007829|PDB:3GBX"
FT STRAND 140..147
FT /evidence="ECO:0007829|PDB:3GBX"
FT HELIX 155..165
FT /evidence="ECO:0007829|PDB:3GBX"
FT STRAND 168..172
FT /evidence="ECO:0007829|PDB:3GBX"
FT HELIX 183..192
FT /evidence="ECO:0007829|PDB:3GBX"
FT STRAND 196..200
FT /evidence="ECO:0007829|PDB:3GBX"
FT TURN 202..204
FT /evidence="ECO:0007829|PDB:3GBX"
FT HELIX 205..209
FT /evidence="ECO:0007829|PDB:3GBX"
FT TURN 217..219
FT /evidence="ECO:0007829|PDB:3GBX"
FT STRAND 220..228
FT /evidence="ECO:0007829|PDB:3GBX"
FT HELIX 229..231
FT /evidence="ECO:0007829|PDB:3GBX"
FT STRAND 237..243
FT /evidence="ECO:0007829|PDB:3GBX"
FT HELIX 246..255
FT /evidence="ECO:0007829|PDB:3GBX"
FT HELIX 266..278
FT /evidence="ECO:0007829|PDB:3GBX"
FT HELIX 282..304
FT /evidence="ECO:0007829|PDB:3GBX"
FT HELIX 310..312
FT /evidence="ECO:0007829|PDB:3GBX"
FT STRAND 315..322
FT /evidence="ECO:0007829|PDB:3GBX"
FT HELIX 324..326
FT /evidence="ECO:0007829|PDB:3GBX"
FT HELIX 330..339
FT /evidence="ECO:0007829|PDB:3GBX"
FT STRAND 345..347
FT /evidence="ECO:0007829|PDB:3GBX"
FT TURN 356..358
FT /evidence="ECO:0007829|PDB:3GBX"
FT STRAND 360..365
FT /evidence="ECO:0007829|PDB:3GBX"
FT HELIX 367..371
FT /evidence="ECO:0007829|PDB:3GBX"
FT HELIX 376..391
FT /evidence="ECO:0007829|PDB:3GBX"
FT TURN 392..394
FT /evidence="ECO:0007829|PDB:3GBX"
FT HELIX 396..412
FT /evidence="ECO:0007829|PDB:3GBX"
SQ SEQUENCE 417 AA; 45455 MW; 3AA2E7EAF302042C CRC64;
MLKREMNIAD YDAELWQAME QEKVRQEEHI ELIASENYTS PRVMQAQGSQ LTNKYAEGYP
GKRYYGGCEY VDVVEQLAID RAKELFGADY ANVQPHSGSQ ANFAVYTALL QPGDTVLGMN
LAQGGHLTHG SPVNFSGKLY NIVPYGIDES GKIDYDEMAK LAKEHKPKMI IGGFSAYSGV
VDWAKMREIA DSIGAYLFVD MAHVAGLIAA GVYPNPVPHA HVVTTTTHKT LAGPRGGLIL
AKGGDEELYK KLNSAVFPSA QGGPLMHVIA GKAVALKEAM EPEFKVYQQQ VAKNAKAMVE
VFLNRGYKVV SGGTENHLFL LDLVDKNLTG KEADAALGRA NITVNKNSVP NDPKSPFVTS
GIRIGSPAVT RRGFKEAEVK ELAGWMCDVL DNINDEATIE RVKAKVLDIC ARFPVYA
