GLYA_HELPY
ID GLYA_HELPY Reviewed; 416 AA.
AC P56089;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 1.
DT 03-AUG-2022, entry version 128.
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=HP_0183;
OS Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori).
OC Bacteria; Proteobacteria; Epsilonproteobacteria; Campylobacterales;
OC Helicobacteraceae; Helicobacter.
OX NCBI_TaxID=85962;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700392 / 26695;
RX PubMed=9252185; DOI=10.1038/41483;
RA Tomb J.-F., White O., Kerlavage A.R., Clayton R.A., Sutton G.G.,
RA Fleischmann R.D., Ketchum K.A., Klenk H.-P., Gill S.R., Dougherty B.A.,
RA Nelson K.E., Quackenbush J., Zhou L., Kirkness E.F., Peterson S.N.,
RA Loftus B.J., Richardson D.L., Dodson R.J., Khalak H.G., Glodek A.,
RA McKenney K., FitzGerald L.M., Lee N., Adams M.D., Hickey E.K., Berg D.E.,
RA Gocayne J.D., Utterback T.R., Peterson J.D., Kelley J.M., Cotton M.D.,
RA Weidman J.F., Fujii C., Bowman C., Watthey L., Wallin E., Hayes W.S.,
RA Borodovsky M., Karp P.D., Smith H.O., Fraser C.M., Venter J.C.;
RT "The complete genome sequence of the gastric pathogen Helicobacter
RT pylori.";
RL Nature 388:539-547(1997).
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; AE000511; AAD07252.1; -; Genomic_DNA.
DR PIR; G64542; G64542.
DR RefSeq; NP_206982.1; NC_000915.1.
DR RefSeq; WP_000323092.1; NC_018939.1.
DR PDB; 6F93; X-ray; 2.80 A; A/B=1-416.
DR PDBsum; 6F93; -.
DR AlphaFoldDB; P56089; -.
DR SMR; P56089; -.
DR DIP; DIP-3405N; -.
DR IntAct; P56089; 1.
DR MINT; P56089; -.
DR STRING; 85962.C694_00910; -.
DR PaxDb; P56089; -.
DR EnsemblBacteria; AAD07252; AAD07252; HP_0183.
DR KEGG; hpy:HP_0183; -.
DR PATRIC; fig|85962.47.peg.198; -.
DR eggNOG; COG0112; Bacteria.
DR OMA; SHPAGLI; -.
DR PhylomeDB; P56089; -.
DR BRENDA; 2.1.2.1; 2604.
DR UniPathway; UPA00193; -.
DR UniPathway; UPA00288; UER01023.
DR Proteomes; UP000000429; 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..416
FT /note="Serine hydroxymethyltransferase"
FT /id="PRO_0000113586"
FT BINDING 118
FT /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57453"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00051"
FT BINDING 122..124
FT /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57453"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00051"
FT BINDING 242
FT /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57453"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00051"
FT BINDING 350..352
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 5..8
FT /evidence="ECO:0007829|PDB:6F93"
FT HELIX 10..24
FT /evidence="ECO:0007829|PDB:6F93"
FT STRAND 25..28
FT /evidence="ECO:0007829|PDB:6F93"
FT HELIX 38..44
FT /evidence="ECO:0007829|PDB:6F93"
FT HELIX 47..49
FT /evidence="ECO:0007829|PDB:6F93"
FT HELIX 70..83
FT /evidence="ECO:0007829|PDB:6F93"
FT STRAND 86..89
FT /evidence="ECO:0007829|PDB:6F93"
FT HELIX 95..106
FT /evidence="ECO:0007829|PDB:6F93"
FT STRAND 112..116
FT /evidence="ECO:0007829|PDB:6F93"
FT STRAND 135..142
FT /evidence="ECO:0007829|PDB:6F93"
FT STRAND 148..150
FT /evidence="ECO:0007829|PDB:6F93"
FT HELIX 152..162
FT /evidence="ECO:0007829|PDB:6F93"
FT STRAND 165..169
FT /evidence="ECO:0007829|PDB:6F93"
FT HELIX 180..190
FT /evidence="ECO:0007829|PDB:6F93"
FT STRAND 193..197
FT /evidence="ECO:0007829|PDB:6F93"
FT TURN 199..201
FT /evidence="ECO:0007829|PDB:6F93"
FT HELIX 202..206
FT /evidence="ECO:0007829|PDB:6F93"
FT TURN 214..216
FT /evidence="ECO:0007829|PDB:6F93"
FT STRAND 218..225
FT /evidence="ECO:0007829|PDB:6F93"
FT HELIX 226..228
FT /evidence="ECO:0007829|PDB:6F93"
FT STRAND 234..239
FT /evidence="ECO:0007829|PDB:6F93"
FT HELIX 241..251
FT /evidence="ECO:0007829|PDB:6F93"
FT STRAND 255..258
FT /evidence="ECO:0007829|PDB:6F93"
FT HELIX 261..275
FT /evidence="ECO:0007829|PDB:6F93"
FT HELIX 277..299
FT /evidence="ECO:0007829|PDB:6F93"
FT HELIX 305..307
FT /evidence="ECO:0007829|PDB:6F93"
FT STRAND 310..317
FT /evidence="ECO:0007829|PDB:6F93"
FT STRAND 321..323
FT /evidence="ECO:0007829|PDB:6F93"
FT HELIX 325..334
FT /evidence="ECO:0007829|PDB:6F93"
FT TURN 351..353
FT /evidence="ECO:0007829|PDB:6F93"
FT STRAND 355..360
FT /evidence="ECO:0007829|PDB:6F93"
FT HELIX 362..366
FT /evidence="ECO:0007829|PDB:6F93"
FT HELIX 371..385
FT /evidence="ECO:0007829|PDB:6F93"
FT TURN 386..389
FT /evidence="ECO:0007829|PDB:6F93"
FT HELIX 391..405
FT /evidence="ECO:0007829|PDB:6F93"
SQ SEQUENCE 416 AA; 45710 MW; 42BB0CD4433CD708 CRC64;
MAYFLEQTDS EIFELIFEEY KRQNEHLEMI ASENYTFASV MEAMGSVLTN KYAEGYPNKR
YYGGCEVVDK IESLAIERAK KLFNCQFANV QAHSGSQANN AVYHALLKPY DKILGMDLSC
GGHLTHGAKV SLTGKHYQSF SYGVNLDGYI DYEEALKIAQ SVKPEIIVCG FSAYPREIDF
KKFREIADEV GALLLGDIAH VAGLVVTGEH AHPFPHCHVV SSTTHKTLRG PRGGIILTND
EEIAAKIDKA IFPGTQGGPL MHVIAAKAVG FKENLKPEFK AYAQLVKSNM QVLAKALKEK
NHKLVSGGTS NHLLLMDFLD KPYSGKDADI ALGNAGITVN KNTIPGETRS PFVTSGIRIG
SAALSARGMG AKEFEIIGNK ISDILNDINN VSLQLHVKEE LKAMVNQFPV YHQPIF
