GLYA_METBF
ID GLYA_METBF Reviewed; 412 AA.
AC Q46A52;
DT 16-MAY-2006, integrated into UniProtKB/Swiss-Prot.
DT 13-SEP-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, ECO:0000269|PubMed:15349715};
GN Name=glyA {ECO:0000255|HAMAP-Rule:MF_00051}; OrderedLocusNames=Mbar_A2316;
OS Methanosarcina barkeri (strain Fusaro / DSM 804).
OC Archaea; Euryarchaeota; Stenosarchaea group; Methanomicrobia;
OC Methanosarcinales; Methanosarcinaceae; Methanosarcina.
OX NCBI_TaxID=269797;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Fusaro / DSM 804;
RX PubMed=16980466; DOI=10.1128/jb.00810-06;
RA Maeder D.L., Anderson I., Brettin T.S., Bruce D.C., Gilna P., Han C.S.,
RA Lapidus A., Metcalf W.W., Saunders E., Tapia R., Sowers K.R.;
RT "The Methanosarcina barkeri genome: comparative analysis with
RT Methanosarcina acetivorans and Methanosarcina mazei reveals extensive
RT rearrangement within methanosarcinal genomes.";
RL J. Bacteriol. 188:7922-7931(2006).
RN [2]
RP PROTEIN SEQUENCE OF 1-13, FUNCTION, THF-DEPENDENT SERINE
RP HYDROXYMETHYLTRANSFERASE ACTIVITY, CATALYTIC ACTIVITY, ALDOLASE ACTIVITY,
RP COFACTOR, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES, AND
RP SUBUNIT.
RC STRAIN=Fusaro / DSM 804;
RX PubMed=15349715; DOI=10.1007/s00203-004-0714-0;
RA Buchenau B., Thauer R.K.;
RT "Tetrahydrofolate-specific enzymes in Methanosarcina barkeri and growth
RT dependence of this methanogenic archaeon on folic acid or p-aminobenzoic
RT acid.";
RL Arch. Microbiol. 182:313-325(2004).
CC -!- FUNCTION: Catalyzes the reversible interconversion of serine and
CC glycine with tetrahydrofolate (THF) serving as the one-carbon carrier.
CC Appears to be specific for THF as the pteridine substrate, since the
CC use of tetrahydromethanopterin (H4MPT) is much less efficient. Also
CC exhibits THF-independent aldolase activity toward beta-hydroxyamino
CC acids, producing glycine and aldehydes, via a retro-aldol mechanism.
CC Thus, is able to catalyze the cleavage of L-allo-threonine and L-threo-
CC beta-phenylserine. {ECO:0000269|PubMed:15349715}.
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 ECO:0000269|PubMed:15349715};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00051,
CC ECO:0000269|PubMed:15349715};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.002 mM for tetrahydrofolate (at pH 7.2 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:15349715};
CC KM=0.2 mM for L-serine (at pH 7.2 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:15349715};
CC KM=2 mM for L-threonine (at pH 7.2 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:15349715};
CC KM=0.3 mM for L-allo-threonine (at pH 7.2 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:15349715};
CC Vmax=6 umol/min/mg enzyme for the serine hydroxymethyltransferase
CC reaction with THF as the pteridine substrate (at pH 7.2 and 37
CC degrees Celsius) {ECO:0000269|PubMed:15349715};
CC Vmax=0.4 umol/min/mg enzyme for the retro-aldol cleavage of L-
CC threonine (at pH 7.2 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:15349715};
CC Vmax=1.6 umol/min/mg enzyme for the retro-aldol cleavage of L-allo-
CC threonine (at pH 7.2 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:15349715};
CC Note=The apparent KM for tetrahydromethanopterin (H4MPT) is superior
CC to 0.3 mM (at pH 7.2 and 37 degrees Celsius).;
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|PubMed:15349715}.
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; CP000099; AAZ71240.1; -; Genomic_DNA.
DR RefSeq; WP_011307286.1; NC_007355.1.
DR AlphaFoldDB; Q46A52; -.
DR SMR; Q46A52; -.
DR STRING; 269797.Mbar_A2316; -.
DR PRIDE; Q46A52; -.
DR EnsemblBacteria; AAZ71240; AAZ71240; Mbar_A2316.
DR GeneID; 3625224; -.
DR KEGG; mba:Mbar_A2316; -.
DR eggNOG; arCOG00070; Archaea.
DR HOGENOM; CLU_022477_2_1_2; -.
DR OMA; SHPAGLI; -.
DR OrthoDB; 22518at2157; -.
DR BRENDA; 2.1.2.1; 3250.
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 Amino-acid biosynthesis; Cytoplasm; Direct protein sequencing;
KW One-carbon metabolism; Pyridoxal phosphate; Transferase.
FT CHAIN 1..412
FT /note="Serine hydroxymethyltransferase"
FT /id="PRO_0000235053"
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 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"
SQ SEQUENCE 412 AA; 45049 MW; 1FDB3BD86045AD7E CRC64;
MSYIEKTDPE LFEAIKKEAE RQEYKLNLIA SENYASKAVM EAQGSILTNK YAEGYSGKRY
YGGCDFVDIA EDLAIARAKK IFNAGYVNVQ PHSGSGANMA VYFSVLKPGD TIMSMDLSHG
GHLSHGSPVS FSGKLFNIVP YGVSKKTEML DYSELMKKAK ENKPQMIVCG ASAYPREIDF
KQFREIADEV GAYLLADIAH IAGLVVAGVH PSPVPYADFV TSTTHKTLRG PRGGIIISKT
EELATRINKA VFPGLQGGPL MHIIAGKAVA FKEAMSEKFK QDQVQTVKNA KTLCKCLKEK
GFDMVSGDTD NHLMLVNLNN MNITGKDAEA ALSKAGIIAN KNTVPFETRS PFITSGVRLG
TPACTTRGMK ETEMELIADY IETAITNSEN DKILSETSDK VRELCSRFPV YC
