GLYA_THET8
ID GLYA_THET8 Reviewed; 407 AA.
AC Q5SI56;
DT 16-MAY-2006, integrated into UniProtKB/Swiss-Prot.
DT 21-DEC-2004, 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=TTHA1524;
OS Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8).
OC Bacteria; Deinococcus-Thermus; Deinococci; Thermales; Thermaceae; Thermus.
OX NCBI_TaxID=300852;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 27634 / DSM 579 / HB8;
RA Masui R., Kurokawa K., Nakagawa N., Tokunaga F., Koyama Y., Shibata T.,
RA Oshima T., Yokoyama S., Yasunaga T., Kuramitsu S.;
RT "Complete genome sequence of Thermus thermophilus HB8.";
RL Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.15 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL PHOSPHATE,
RP AND SUBUNIT.
RG RIKEN structural genomics initiative (RSGI);
RT "Crystal structure of t.th.hb8 serine hydroxymethyltransferase.";
RL Submitted (JUL-2011) 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; AP008226; BAD71347.1; -; Genomic_DNA.
DR RefSeq; WP_011228734.1; NC_006461.1.
DR RefSeq; YP_144790.1; NC_006461.1.
DR PDB; 2DKJ; X-ray; 1.15 A; A/B=1-407.
DR PDBsum; 2DKJ; -.
DR AlphaFoldDB; Q5SI56; -.
DR SMR; Q5SI56; -.
DR STRING; 300852.55772906; -.
DR EnsemblBacteria; BAD71347; BAD71347; BAD71347.
DR GeneID; 3169745; -.
DR KEGG; ttj:TTHA1524; -.
DR PATRIC; fig|300852.9.peg.1499; -.
DR eggNOG; COG0112; Bacteria.
DR HOGENOM; CLU_022477_2_1_0; -.
DR OMA; SHPAGLI; -.
DR PhylomeDB; Q5SI56; -.
DR BRENDA; 2.1.2.1; 2305.
DR UniPathway; UPA00193; -.
DR UniPathway; UPA00288; UER01023.
DR EvolutionaryTrace; Q5SI56; -.
DR Proteomes; UP000000532; 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; Reference proteome; Transferase.
FT CHAIN 1..407
FT /note="Serine hydroxymethyltransferase"
FT /id="PRO_0000235042"
FT BINDING 51
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000269|Ref.2"
FT BINDING 94..95
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000269|Ref.2"
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 BINDING 172
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000269|Ref.2"
FT BINDING 200
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000269|Ref.2"
FT BINDING 225
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000269|Ref.2"
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 258
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000269|Ref.2"
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 ECO:0000269|Ref.2"
FT HELIX 9..23
FT /evidence="ECO:0007829|PDB:2DKJ"
FT STRAND 25..27
FT /evidence="ECO:0007829|PDB:2DKJ"
FT HELIX 37..43
FT /evidence="ECO:0007829|PDB:2DKJ"
FT HELIX 46..49
FT /evidence="ECO:0007829|PDB:2DKJ"
FT STRAND 58..62
FT /evidence="ECO:0007829|PDB:2DKJ"
FT HELIX 65..82
FT /evidence="ECO:0007829|PDB:2DKJ"
FT STRAND 85..88
FT /evidence="ECO:0007829|PDB:2DKJ"
FT HELIX 94..105
FT /evidence="ECO:0007829|PDB:2DKJ"
FT STRAND 111..115
FT /evidence="ECO:0007829|PDB:2DKJ"
FT HELIX 117..119
FT /evidence="ECO:0007829|PDB:2DKJ"
FT HELIX 123..125
FT /evidence="ECO:0007829|PDB:2DKJ"
FT HELIX 131..135
FT /evidence="ECO:0007829|PDB:2DKJ"
FT STRAND 136..141
FT /evidence="ECO:0007829|PDB:2DKJ"
FT TURN 145..147
FT /evidence="ECO:0007829|PDB:2DKJ"
FT HELIX 152..162
FT /evidence="ECO:0007829|PDB:2DKJ"
FT STRAND 165..169
FT /evidence="ECO:0007829|PDB:2DKJ"
FT HELIX 180..190
FT /evidence="ECO:0007829|PDB:2DKJ"
FT STRAND 193..197
FT /evidence="ECO:0007829|PDB:2DKJ"
FT TURN 199..201
FT /evidence="ECO:0007829|PDB:2DKJ"
FT HELIX 202..206
FT /evidence="ECO:0007829|PDB:2DKJ"
FT TURN 214..216
FT /evidence="ECO:0007829|PDB:2DKJ"
FT STRAND 218..225
FT /evidence="ECO:0007829|PDB:2DKJ"
FT HELIX 226..228
FT /evidence="ECO:0007829|PDB:2DKJ"
FT STRAND 234..239
FT /evidence="ECO:0007829|PDB:2DKJ"
FT HELIX 241..251
FT /evidence="ECO:0007829|PDB:2DKJ"
FT TURN 252..255
FT /evidence="ECO:0007829|PDB:2DKJ"
FT HELIX 261..275
FT /evidence="ECO:0007829|PDB:2DKJ"
FT HELIX 277..299
FT /evidence="ECO:0007829|PDB:2DKJ"
FT HELIX 305..307
FT /evidence="ECO:0007829|PDB:2DKJ"
FT STRAND 310..317
FT /evidence="ECO:0007829|PDB:2DKJ"
FT HELIX 319..321
FT /evidence="ECO:0007829|PDB:2DKJ"
FT HELIX 325..334
FT /evidence="ECO:0007829|PDB:2DKJ"
FT TURN 351..353
FT /evidence="ECO:0007829|PDB:2DKJ"
FT STRAND 355..360
FT /evidence="ECO:0007829|PDB:2DKJ"
FT HELIX 362..366
FT /evidence="ECO:0007829|PDB:2DKJ"
FT HELIX 371..373
FT /evidence="ECO:0007829|PDB:2DKJ"
FT HELIX 374..387
FT /evidence="ECO:0007829|PDB:2DKJ"
FT HELIX 391..402
FT /evidence="ECO:0007829|PDB:2DKJ"
SQ SEQUENCE 407 AA; 44619 MW; CEF220A3E20179A0 CRC64;
MVSTLKRDEA LFELIALEEK RQREGLELIA SENFVSKQVR EAVGSVLTNK YAEGYPGARY
YGGCEVIDRV ESLAIERAKA LFGAAWANVQ PHSGSQANMA VYMALMEPGD TLMGMDLAAG
GHLTHGSRVN FSGKLYKVVS YGVRPDTELI DLEEVRRLAL EHRPKVIVAG ASAYPRFWDF
KAFREIADEV GAYLVVDMAH FAGLVAAGLH PNPLPYAHVV TSTTHKTLRG PRGGLILSND
PELGKRIDKL IFPGIQGGPL EHVIAGKAVA FFEALQPEFK EYSRLVVENA KRLAEELARR
GYRIVTGGTD NHLFLVDLRP KGLTGKEAEE RLDAVGITVN KNAIPFDPKP PRVTSGIRIG
TPAITTRGFT PEEMPLVAEL IDRALLEGPS EALREEVRRL ALAHPMP
