GLYA_METJA
ID GLYA_METJA Reviewed; 429 AA.
AC Q58992;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 1.
DT 03-AUG-2022, entry version 132.
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.- {ECO:0000255|HAMAP-Rule:MF_00051, ECO:0000269|PubMed:12902326};
DE AltName: Full=L-allo-threonine aldolase;
DE EC=4.1.2.49;
GN Name=glyA {ECO:0000255|HAMAP-Rule:MF_00051}; OrderedLocusNames=MJ1597;
OS Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM
OS 10045 / NBRC 100440) (Methanococcus jannaschii).
OC Archaea; Euryarchaeota; Methanomada group; Methanococci; Methanococcales;
OC Methanocaldococcaceae; Methanocaldococcus.
OX NCBI_TaxID=243232;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440;
RX PubMed=8688087; DOI=10.1126/science.273.5278.1058;
RA Bult C.J., White O., Olsen G.J., Zhou L., Fleischmann R.D., Sutton G.G.,
RA Blake J.A., FitzGerald L.M., Clayton R.A., Gocayne J.D., Kerlavage A.R.,
RA Dougherty B.A., Tomb J.-F., Adams M.D., Reich C.I., Overbeek R.,
RA Kirkness E.F., Weinstock K.G., Merrick J.M., Glodek A., Scott J.L.,
RA Geoghagen N.S.M., Weidman J.F., Fuhrmann J.L., Nguyen D., Utterback T.R.,
RA Kelley J.M., Peterson J.D., Sadow P.W., Hanna M.C., Cotton M.D.,
RA Roberts K.M., Hurst M.A., Kaine B.P., Borodovsky M., Klenk H.-P.,
RA Fraser C.M., Smith H.O., Woese C.R., Venter J.C.;
RT "Complete genome sequence of the methanogenic archaeon, Methanococcus
RT jannaschii.";
RL Science 273:1058-1073(1996).
RN [2]
RP FUNCTION, H4MPT-DEPENDENT SERINE HYDROXYMETHYLTRANSFERASE ACTIVITY,
RP CATALYTIC ACTIVITY, ALDOLASE ACTIVITY, COFACTOR, SUBSTRATE SPECIFICITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, AND SUBUNIT.
RC STRAIN=ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440;
RX PubMed=12902326; DOI=10.1074/jbc.m306747200;
RA Angelaccio S., Chiaraluce R., Consalvi V., Buchenau B., Giangiacomo L.,
RA Bossa F., Contestabile R.;
RT "Catalytic and thermodynamic properties of tetrahydromethanopterin-
RT dependent serine hydroxymethyltransferase from Methanococcus jannaschii.";
RL J. Biol. Chem. 278:41789-41797(2003).
CC -!- FUNCTION: Catalyzes the reversible interconversion of serine and
CC glycine with tetrahydromethanopterin (H4MPT) serving as the one-carbon
CC carrier. The use of tetrahydrofolate (THF or H4PteGlu) as the pteridine
CC substrate is 450-fold less efficient than that of H4MPT. Also exhibits
CC a pteridine-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:12902326}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5,10-methylenetetrahydromethanopterin + glycine + H2O =
CC 5,6,7,8-tetrahydromethanopterin + L-serine; Xref=Rhea:RHEA:47104,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:33384, ChEBI:CHEBI:57305,
CC ChEBI:CHEBI:57818, ChEBI:CHEBI:58103; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_00051, ECO:0000269|PubMed:12902326};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-allo-threonine = acetaldehyde + glycine;
CC Xref=Rhea:RHEA:26209, ChEBI:CHEBI:15343, ChEBI:CHEBI:57305,
CC ChEBI:CHEBI:58585; EC=4.1.2.49;
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00051,
CC ECO:0000269|PubMed:12902326};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.8 mM for L-serine (at 37 degrees Celsius)
CC {ECO:0000269|PubMed:12902326};
CC KM=0.1 mM for tetrahydromethanopterin (at 37 degrees Celsius)
CC {ECO:0000269|PubMed:12902326};
CC KM=1.3 mM for L-allo-threonine (at 60 degrees Celsius)
CC {ECO:0000269|PubMed:12902326};
CC KM=95 mM for DL-threo-beta-phenylserine (at 60 degrees Celsius)
CC {ECO:0000269|PubMed:12902326};
CC Note=kcat is 212 min(-1) for the L-serine hydroxymethyltransferase
CC reaction, and 687 min(-1) for the L-allo-threonine cleavage, at 37
CC and 60 degrees Celsius, respectively. The presence of oxygen does not
CC seem to affect significantly the kinetic parameters of the
CC reactions.;
CC Temperature dependence:
CC Optimum temperature is 70-80 degrees Celsius for the retro-aldol
CC cleavage of L-allo-threonine. {ECO:0000269|PubMed:12902326};
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:12902326}.
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; L77117; AAB99615.1; -; Genomic_DNA.
DR PIR; D64499; D64499.
DR RefSeq; WP_010871121.1; NC_000909.1.
DR PDB; 4BHD; X-ray; 2.83 A; A/B=3-429.
DR PDB; 4UQV; X-ray; 3.00 A; A/B/C/D/E/F/G/H/I/J/K/L=1-429.
DR PDBsum; 4BHD; -.
DR PDBsum; 4UQV; -.
DR AlphaFoldDB; Q58992; -.
DR SMR; Q58992; -.
DR STRING; 243232.MJ_1597; -.
DR EnsemblBacteria; AAB99615; AAB99615; MJ_1597.
DR GeneID; 1452505; -.
DR KEGG; mja:MJ_1597; -.
DR eggNOG; arCOG00070; Archaea.
DR HOGENOM; CLU_022477_2_1_2; -.
DR InParanoid; Q58992; -.
DR OMA; SHPAGLI; -.
DR OrthoDB; 22518at2157; -.
DR PhylomeDB; Q58992; -.
DR BRENDA; 2.1.2.1; 3260.
DR UniPathway; UPA00288; UER01023.
DR Proteomes; UP000000805; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0004372; F:glycine hydroxymethyltransferase activity; IBA:GO_Central.
DR GO; GO:0008732; F:L-allo-threonine aldolase activity; IEA:UniProtKB-EC.
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:InterPro.
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; Lyase;
KW One-carbon metabolism; Pyridoxal phosphate; Reference proteome;
KW Transferase.
FT CHAIN 1..429
FT /note="Serine hydroxymethyltransferase"
FT /id="PRO_0000113713"
FT BINDING 120..122
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 3..5
FT /evidence="ECO:0007829|PDB:4UQV"
FT HELIX 6..22
FT /evidence="ECO:0007829|PDB:4BHD"
FT STRAND 24..26
FT /evidence="ECO:0007829|PDB:4BHD"
FT HELIX 36..43
FT /evidence="ECO:0007829|PDB:4BHD"
FT HELIX 45..47
FT /evidence="ECO:0007829|PDB:4UQV"
FT STRAND 60..62
FT /evidence="ECO:0007829|PDB:4UQV"
FT HELIX 65..81
FT /evidence="ECO:0007829|PDB:4BHD"
FT STRAND 84..87
FT /evidence="ECO:0007829|PDB:4BHD"
FT HELIX 93..104
FT /evidence="ECO:0007829|PDB:4BHD"
FT STRAND 111..113
FT /evidence="ECO:0007829|PDB:4BHD"
FT TURN 116..119
FT /evidence="ECO:0007829|PDB:4BHD"
FT HELIX 122..124
FT /evidence="ECO:0007829|PDB:4BHD"
FT TURN 130..132
FT /evidence="ECO:0007829|PDB:4BHD"
FT STRAND 137..139
FT /evidence="ECO:0007829|PDB:4BHD"
FT TURN 144..147
FT /evidence="ECO:0007829|PDB:4BHD"
FT HELIX 151..161
FT /evidence="ECO:0007829|PDB:4BHD"
FT STRAND 164..168
FT /evidence="ECO:0007829|PDB:4BHD"
FT HELIX 179..189
FT /evidence="ECO:0007829|PDB:4BHD"
FT STRAND 192..196
FT /evidence="ECO:0007829|PDB:4BHD"
FT TURN 198..200
FT /evidence="ECO:0007829|PDB:4BHD"
FT HELIX 201..205
FT /evidence="ECO:0007829|PDB:4BHD"
FT HELIX 212..214
FT /evidence="ECO:0007829|PDB:4BHD"
FT STRAND 218..223
FT /evidence="ECO:0007829|PDB:4BHD"
FT STRAND 226..228
FT /evidence="ECO:0007829|PDB:4BHD"
FT STRAND 234..238
FT /evidence="ECO:0007829|PDB:4BHD"
FT HELIX 240..249
FT /evidence="ECO:0007829|PDB:4BHD"
FT STRAND 250..254
FT /evidence="ECO:0007829|PDB:4UQV"
FT HELIX 262..296
FT /evidence="ECO:0007829|PDB:4BHD"
FT TURN 297..299
FT /evidence="ECO:0007829|PDB:4BHD"
FT HELIX 305..307
FT /evidence="ECO:0007829|PDB:4BHD"
FT STRAND 311..319
FT /evidence="ECO:0007829|PDB:4BHD"
FT TURN 323..325
FT /evidence="ECO:0007829|PDB:4BHD"
FT HELIX 329..338
FT /evidence="ECO:0007829|PDB:4BHD"
FT STRAND 344..346
FT /evidence="ECO:0007829|PDB:4BHD"
FT STRAND 360..365
FT /evidence="ECO:0007829|PDB:4BHD"
FT HELIX 367..371
FT /evidence="ECO:0007829|PDB:4BHD"
FT HELIX 376..390
FT /evidence="ECO:0007829|PDB:4BHD"
FT HELIX 396..408
FT /evidence="ECO:0007829|PDB:4BHD"
FT STRAND 415..418
FT /evidence="ECO:0007829|PDB:4BHD"
FT STRAND 421..423
FT /evidence="ECO:0007829|PDB:4UQV"
SQ SEQUENCE 429 AA; 48084 MW; C115CECA4E649C7A CRC64;
MEYSDVPKFI RDVSIKQHEW MRESIKLIAS ENITSLAVRE ACATDFMHRY AEGLPGKRLY
QGCKYIDEVE TLCIELSKEL FKAEHANVQP TSGVVANLAV FFAETKPGDK LMALSVPDGG
HISHWKVSAA GIRGLKVINH PFDPEEMNID ADAMVKKILE EKPKLILFGG SLFPFPHPVA
DAYEAAQEVG AKIAYDGAHV LGLIAGKQFQ DPLREGAEYL MGSTHKTFFG PQGGVILTTK
ENADKIDSHV FPGVVSNHHL HHKAGLAIAL AEMLEFGEAY AKQVIKNAKA LAQALYERGF
NVLCEHKDFT ESHQVIIDIE SSPDIEFSAS ELAKMYEEAN IILNKNLLPW DDVNNSDNPS
GIRLGTQECT RLGMKEKEME EIAEFMKRIA IDKEKPEKVR EDVKEFAKEY STIHYSFDEG
DGFKYLRFY
