ID A0A139TPW3_9BACT Unreviewed; 575 AA.
AC A0A139TPW3;
DT 08-JUN-2016, integrated into UniProtKB/TrEMBL.
DT 08-JUN-2016, sequence version 1.
DT 27-MAR-2024, entry version 30.
DE RecName: Full=Serine hydroxymethyltransferase {ECO:0000256|HAMAP-Rule:MF_00051};
DE Short=SHMT {ECO:0000256|HAMAP-Rule:MF_00051};
DE Short=Serine methylase {ECO:0000256|HAMAP-Rule:MF_00051};
DE EC=2.1.2.1 {ECO:0000256|HAMAP-Rule:MF_00051};
GN Name=glyA {ECO:0000256|HAMAP-Rule:MF_00051};
GN ORFNames=HMPREF3039_02352 {ECO:0000313|EMBL:KXU53629.1};
OS Akkermansia sp. KLE1798.
OC Bacteria; Verrucomicrobiota; Verrucomicrobiae; Verrucomicrobiales;
OC Akkermansiaceae; Akkermansia.
OX NCBI_TaxID=1574265 {ECO:0000313|EMBL:KXU53629.1, ECO:0000313|Proteomes:UP000070454};
RN [1] {ECO:0000313|EMBL:KXU53629.1, ECO:0000313|Proteomes:UP000070454}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=KLE1798 {ECO:0000313|EMBL:KXU53629.1,
RC ECO:0000313|Proteomes:UP000070454};
RA Wen L., He K., Yang H.;
RL Submitted (FEB-2016) to the EMBL/GenBank/DDBJ databases.
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:0000256|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:0000256|HAMAP-Rule:MF_00051};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000256|ARBA:ARBA00001933,
CC ECO:0000256|HAMAP-Rule:MF_00051};
CC -!- PATHWAY: Amino-acid biosynthesis; glycine biosynthesis; glycine from L-
CC serine: step 1/1. {ECO:0000256|HAMAP-Rule:MF_00051}.
CC -!- PATHWAY: One-carbon metabolism; tetrahydrofolate interconversion.
CC {ECO:0000256|HAMAP-Rule:MF_00051}.
CC -!- SUBUNIT: Homodimer. {ECO:0000256|ARBA:ARBA00011738, ECO:0000256|HAMAP-
CC Rule:MF_00051}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00051}.
CC -!- SIMILARITY: Belongs to the LacAB/RpiB family.
CC {ECO:0000256|ARBA:ARBA00008754}.
CC -!- SIMILARITY: Belongs to the SHMT family. {ECO:0000256|ARBA:ARBA00006376,
CC ECO:0000256|HAMAP-Rule:MF_00051}.
CC -!- CAUTION: Lacks conserved residue(s) required for the propagation of
CC feature annotation. {ECO:0000256|HAMAP-Rule:MF_00051}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:KXU53629.1}.
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DR EMBL; LTZM01000048; KXU53629.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A139TPW3; -.
DR PATRIC; fig|1574265.3.peg.2292; -.
DR UniPathway; UPA00193; -.
DR UniPathway; UPA00288; UER01023.
DR Proteomes; UP000070454; Unassembled WGS sequence.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0004372; F:glycine hydroxymethyltransferase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0016861; F:intramolecular oxidoreductase activity, interconverting aldoses and ketoses; IEA:UniProt.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IEA:UniProtKB-UniRule.
DR GO; GO:0005975; P:carbohydrate metabolic process; IEA:InterPro.
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; 3.90.1150.10; Aspartate Aminotransferase, domain 1; 1.
DR Gene3D; 3.40.1400.10; Sugar-phosphate isomerase, RpiB/LacA/LacB; 1.
DR Gene3D; 3.40.640.10; Type I PLP-dependent aspartate aminotransferase-like (Major domain); 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; IPR004785; RpiB.
DR InterPro; IPR003500; RpiB_LacA_LacB.
DR InterPro; IPR036569; RpiB_LacA_LacB_sf.
DR InterPro; IPR001085; Ser_HO-MeTrfase.
DR InterPro; IPR019798; Ser_HO-MeTrfase_PLP_BS.
DR InterPro; IPR039429; SHMT-like_dom.
DR NCBIfam; TIGR01120; rpiB; 1.
DR NCBIfam; TIGR00689; rpiB_lacA_lacB; 1.
DR PANTHER; PTHR11680; SERINE HYDROXYMETHYLTRANSFERASE; 1.
DR PANTHER; PTHR11680:SF28; SERINE HYDROXYMETHYLTRANSFERASE; 1.
DR Pfam; PF02502; LacAB_rpiB; 1.
DR Pfam; PF00464; SHMT; 1.
DR SUPFAM; SSF53383; PLP-dependent transferases; 1.
DR SUPFAM; SSF89623; Ribose/Galactose isomerase RpiB/AlsB; 1.
DR PROSITE; PS00096; SHMT; 1.
PE 3: Inferred from homology;
KW Amino-acid biosynthesis {ECO:0000256|HAMAP-Rule:MF_00051};
KW Cytoplasm {ECO:0000256|ARBA:ARBA00022490, ECO:0000256|HAMAP-Rule:MF_00051};
KW Isomerase {ECO:0000313|EMBL:KXU53629.1};
KW One-carbon metabolism {ECO:0000256|ARBA:ARBA00022563, ECO:0000256|HAMAP-
KW Rule:MF_00051};
KW Pyridoxal phosphate {ECO:0000256|ARBA:ARBA00022898, ECO:0000256|HAMAP-
KW Rule:MF_00051};
KW Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000256|HAMAP-
KW Rule:MF_00051}.
FT DOMAIN 163..538
FT /note="Serine hydroxymethyltransferase-like"
FT /evidence="ECO:0000259|Pfam:PF00464"
FT BINDING 275
FT /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57453"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00051"
FT BINDING 279..281
FT /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57453"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00051"
FT BINDING 398
FT /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57453"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00051"
FT SITE 383
FT /note="Plays an important role in substrate specificity"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00051"
FT MOD_RES 384
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00051"
SQ SEQUENCE 575 AA; 62270 MW; 974F6C35225A4301 CRC64;
MRQNISPPAI CTIMNTTFKI AIGSDHAGVD LKETIVELLK AWGHEVTDMG TETKNSCDYS
DYANAVASSI ADGTNERGIL ICRSGIGMSI AANRWVGVRA ALCRTAPAAA LSRQHNNSNL
LCLASAYVDN ESVEDVLDAW LHADFEGGRH ERRVVKSSGS PLQWSDPELA AFIEEEGRRQ
SNNIELIASE NFASPSVREA QGSLLTNKYA EGYPGKRWYG GCEVVDKVEQ LAIDRVLKLF
GGEHANVQPH SGSQANMAVY FSVLKPGDTI LTMDLSHGGH LTHGHRANFS GKLYNVVHYG
VSQESEAIDY DALEKLAMEV KPNMITAGAS AYSRTIDFER MAKIARACGA YLFVDMAHIA
GLVAGGQHPN PVPHADFVAS TTHKSLRGPR GGFIICKEEY AKKIDAAVFP GMQGGPLMHV
IAAKAACFGE ALKPEFKDYA AQVVKNAQAM SKKMTELGFR VVSNGTDNHV FMVDLRNKGI
NGAEAQEALD RVGITVNKNA IPFDTGSPMK PSGIRIGTPA VTTRGMKEQD VEQVAEFIAR
ALALHVGEQV CPNPEGFSQL KKEVSAFNRN FRLPH
//
