GLYA_STRT1
ID GLYA_STRT1 Reviewed; 416 AA.
AC Q5M0B4;
DT 16-MAY-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-2005, sequence version 1.
DT 03-AUG-2022, entry version 104.
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=str0755;
OS Streptococcus thermophilus (strain CNRZ 1066).
OC Bacteria; Firmicutes; Bacilli; Lactobacillales; Streptococcaceae;
OC Streptococcus.
OX NCBI_TaxID=299768;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=CNRZ 1066;
RX PubMed=15543133; DOI=10.1038/nbt1034;
RA Bolotin A., Quinquis B., Renault P., Sorokin A., Ehrlich S.D.,
RA Kulakauskas S., Lapidus A., Goltsman E., Mazur M., Pusch G.D., Fonstein M.,
RA Overbeek R., Kyprides N., Purnelle B., Prozzi D., Ngui K., Masuy D.,
RA Hancy F., Burteau S., Boutry M., Delcour J., Goffeau A., Hols P.;
RT "Complete sequence and comparative genome analysis of the dairy bacterium
RT Streptococcus thermophilus.";
RL Nat. Biotechnol. 22:1554-1558(2004).
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; CP000024; AAV62348.1; -; Genomic_DNA.
DR RefSeq; WP_011227085.1; NC_006449.1.
DR PDB; 4WXB; X-ray; 2.05 A; A/B/C/D=1-416.
DR PDB; 4WXF; X-ray; 2.40 A; A/C=1-416.
DR PDB; 4WXG; X-ray; 2.00 A; A/C=1-416.
DR PDB; 6TGH; X-ray; 2.12 A; A/B/C/D=2-416.
DR PDB; 6TI1; X-ray; 2.00 A; A/C=1-416.
DR PDB; 6TI3; X-ray; 1.96 A; A/B/C/D=1-416.
DR PDB; 6YRW; X-ray; 2.50 A; A/B/C/D=1-416.
DR PDBsum; 4WXB; -.
DR PDBsum; 4WXF; -.
DR PDBsum; 4WXG; -.
DR PDBsum; 6TGH; -.
DR PDBsum; 6TI1; -.
DR PDBsum; 6TI3; -.
DR PDBsum; 6YRW; -.
DR AlphaFoldDB; Q5M0B4; -.
DR SMR; Q5M0B4; -.
DR KEGG; stc:str0755; -.
DR HOGENOM; CLU_022477_2_1_9; -.
DR OMA; SHPAGLI; -.
DR BRENDA; 2.1.2.1; 5956.
DR UniPathway; UPA00193; -.
DR UniPathway; UPA00288; UER01023.
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..416
FT /note="Serine hydroxymethyltransferase"
FT /id="PRO_0000235033"
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 229
FT /note="Plays an important role in substrate specificity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00051"
FT MOD_RES 230
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00051"
FT TURN 8..10
FT /evidence="ECO:0007829|PDB:6TI3"
FT HELIX 13..27
FT /evidence="ECO:0007829|PDB:6TI3"
FT STRAND 29..31
FT /evidence="ECO:0007829|PDB:4WXG"
FT HELIX 41..47
FT /evidence="ECO:0007829|PDB:6TI3"
FT HELIX 50..53
FT /evidence="ECO:0007829|PDB:6TI3"
FT STRAND 62..67
FT /evidence="ECO:0007829|PDB:6TI3"
FT HELIX 69..86
FT /evidence="ECO:0007829|PDB:6TI3"
FT STRAND 89..92
FT /evidence="ECO:0007829|PDB:6TI3"
FT HELIX 98..109
FT /evidence="ECO:0007829|PDB:6TI3"
FT STRAND 115..119
FT /evidence="ECO:0007829|PDB:6TI3"
FT TURN 121..124
FT /evidence="ECO:0007829|PDB:6TI3"
FT HELIX 127..129
FT /evidence="ECO:0007829|PDB:6TI3"
FT HELIX 135..139
FT /evidence="ECO:0007829|PDB:6TI3"
FT STRAND 140..145
FT /evidence="ECO:0007829|PDB:6TI3"
FT TURN 149..151
FT /evidence="ECO:0007829|PDB:6TI3"
FT HELIX 156..166
FT /evidence="ECO:0007829|PDB:6TI3"
FT STRAND 169..173
FT /evidence="ECO:0007829|PDB:6TI3"
FT HELIX 184..193
FT /evidence="ECO:0007829|PDB:6TI3"
FT STRAND 197..201
FT /evidence="ECO:0007829|PDB:6TI3"
FT TURN 203..205
FT /evidence="ECO:0007829|PDB:6TI3"
FT HELIX 206..210
FT /evidence="ECO:0007829|PDB:6TI3"
FT TURN 218..220
FT /evidence="ECO:0007829|PDB:6TI3"
FT STRAND 222..230
FT /evidence="ECO:0007829|PDB:6TI3"
FT STRAND 238..243
FT /evidence="ECO:0007829|PDB:6TI3"
FT HELIX 245..255
FT /evidence="ECO:0007829|PDB:6TI3"
FT TURN 256..259
FT /evidence="ECO:0007829|PDB:6TI3"
FT HELIX 265..279
FT /evidence="ECO:0007829|PDB:6TI3"
FT HELIX 281..303
FT /evidence="ECO:0007829|PDB:6TI3"
FT STRAND 304..306
FT /evidence="ECO:0007829|PDB:4WXF"
FT HELIX 310..312
FT /evidence="ECO:0007829|PDB:6TI3"
FT STRAND 315..322
FT /evidence="ECO:0007829|PDB:6TI3"
FT TURN 324..326
FT /evidence="ECO:0007829|PDB:6TI3"
FT STRAND 327..329
FT /evidence="ECO:0007829|PDB:6YRW"
FT HELIX 330..338
FT /evidence="ECO:0007829|PDB:6TI3"
FT TURN 339..341
FT /evidence="ECO:0007829|PDB:6TI3"
FT STRAND 345..347
FT /evidence="ECO:0007829|PDB:4WXG"
FT TURN 356..358
FT /evidence="ECO:0007829|PDB:6TI3"
FT STRAND 360..365
FT /evidence="ECO:0007829|PDB:6TI3"
FT HELIX 367..371
FT /evidence="ECO:0007829|PDB:6TI3"
FT HELIX 376..391
FT /evidence="ECO:0007829|PDB:6TI3"
FT TURN 392..394
FT /evidence="ECO:0007829|PDB:6TI3"
FT HELIX 396..412
FT /evidence="ECO:0007829|PDB:6TI3"
SQ SEQUENCE 416 AA; 45086 MW; 2F6437A39A42094A CRC64;
MIFDKEDYKA FDPELWNAID AEAERQQNNI ELIASENVVS KAVMAAQGTL LTNKYAEGYP
GKRYYGGTAV IDVVETLAIE RAKKLFGAKF ANVQPHSGSQ ANAAVYMSLI QPGDTVMGMD
LSAGGHLTHG APVSFSGKTY NFVSYNVDKE SELLDYDAIL AQAKEVRPKL IVAGASAYSR
IIDFAKFREI ADAVGAYLMV DMAHIAGLVA SGHHPSPVPY AHVTTTTTHK TLRGPRGGLI
LTDDEDIAKK LNSAVFPGLQ GGPLEHVIAA KAVALKEALD PAFKEYGENV IKNAAAMADV
FNQHPDFRVI SGGTNNHLFL VDVTKVVENG KVAQNVLEEV NITLNKNSIP YEQLSPFKTS
GIRVGSPAIT SRGMGEAESR QIAEWMVEAL ENHDKPEVLE RIRGDVKVLT DAFPLY
