ID A0A1B9N7Y7_9MICO Unreviewed; 432 AA.
AC A0A1B9N7Y7;
DT 02-NOV-2016, integrated into UniProtKB/TrEMBL.
DT 02-NOV-2016, sequence version 1.
DT 27-MAR-2024, entry version 32.
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=A7J15_10705 {ECO:0000313|EMBL:OCG72698.1}, E3O41_10525
GN {ECO:0000313|EMBL:QBR74789.1};
OS Microbacterium sediminis.
OC Bacteria; Actinomycetota; Actinomycetes; Micrococcales; Microbacteriaceae;
OC Microbacterium.
OX NCBI_TaxID=904291 {ECO:0000313|EMBL:OCG72698.1, ECO:0000313|Proteomes:UP000093355};
RN [1] {ECO:0000313|EMBL:OCG72698.1, ECO:0000313|Proteomes:UP000093355}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=YLB-01 {ECO:0000313|EMBL:OCG72698.1,
RC ECO:0000313|Proteomes:UP000093355};
RA Lavstsen T., Jespersen J.S.;
RL Submitted (MAY-2016) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:QBR74789.1, ECO:0000313|Proteomes:UP000295661}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=YLB-01 {ECO:0000313|EMBL:QBR74789.1,
RC ECO:0000313|Proteomes:UP000295661};
RA Yu L.;
RL Submitted (MAR-2019) to the EMBL/GenBank/DDBJ databases.
RN [3] {ECO:0000313|EMBL:QBR74789.1, ECO:0000313|Proteomes:UP000295661}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=YLB-01 {ECO:0000313|EMBL:QBR74789.1,
RC ECO:0000313|Proteomes:UP000295661};
RA Xu X.;
RT "Genomic analysis of Microbacterium sediminis YLB-01 reveals backgrounds
RT related to its deep sea enviroment adaptation.";
RL Submitted (APR-2019) 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, ECO:0000256|PIRSR:PIRSR000412-50};
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 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}.
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DR EMBL; LXMD01000029; OCG72698.1; -; Genomic_DNA.
DR EMBL; CP038256; QBR74789.1; -; Genomic_DNA.
DR RefSeq; WP_067027780.1; NZ_KV744789.1.
DR AlphaFoldDB; A0A1B9N7Y7; -.
DR STRING; 904291.A7J15_10705; -.
DR KEGG; msed:E3O41_10525; -.
DR OrthoDB; 9803846at2; -.
DR UniPathway; UPA00193; -.
DR UniPathway; UPA00288; UER01023.
DR Proteomes; UP000093355; Unassembled WGS sequence.
DR Proteomes; UP000295661; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0004372; F:glycine hydroxymethyltransferase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0008168; F:methyltransferase activity; IEA:UniProtKB-KW.
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:0032259; P:methylation; IEA:UniProtKB-KW.
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; 3.40.640.10; 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; IPR001085; Ser_HO-MeTrfase.
DR InterPro; IPR019798; Ser_HO-MeTrfase_PLP_BS.
DR InterPro; IPR039429; SHMT-like_dom.
DR PANTHER; PTHR11680; SERINE HYDROXYMETHYLTRANSFERASE; 1.
DR PANTHER; PTHR11680:SF28; SERINE HYDROXYMETHYLTRANSFERASE; 1.
DR Pfam; PF00464; SHMT; 1.
DR PIRSF; PIRSF000412; SHMT; 1.
DR SUPFAM; SSF53383; PLP-dependent transferases; 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 Methyltransferase {ECO:0000313|EMBL:OCG72698.1};
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}; Reference proteome {ECO:0000313|Proteomes:UP000093355};
KW Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000256|HAMAP-
KW Rule:MF_00051}.
FT DOMAIN 10..392
FT /note="Serine hydroxymethyltransferase-like"
FT /evidence="ECO:0000259|Pfam:PF00464"
FT BINDING 123
FT /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57453"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00051"
FT BINDING 127..129
FT /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57453"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00051"
FT SITE 231
FT /note="Plays an important role in substrate specificity"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00051"
FT MOD_RES 232
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00051,
FT ECO:0000256|PIRSR:PIRSR000412-50"
SQ SEQUENCE 432 AA; 46335 MW; 44C2293FE9DF1342 CRC64;
MTDPLFNAPL AEVDPEIAQV LQRELDRQRG FLEMIASENF VPLSVLQSQG SVLTNKYAEG
YPGRRYYGGC EEVDVAENLA IERAKALFGA EFANVQPHSG ASANAAVLHA IARPGDTILG
LSLDHGGHLT HGMKINFSGR LYNVVPYEVD PETSMVDMDE VRRLAIEHQP KVIIAGWSAY
PRQLDFAAFR AIADEVGALL WVDMAHFAGL VAAGLHPSPV PHAHVVSSTV HKTIGGPRSG
FILTNDADLA KKINTAVFPG QQGGPLMHVI AAKATAFKLA ATPEFRDRQE RTLRGARILA
ERLTRQDVTD AGIAVRSGGT DVHLVLVDLR DAAIDGKQAE DLLHEIRITV NRNSVPNDPR
PPMITSGLRI GTPALATRGF GDAEFTEVAD IIALALLPDP DIAALRARVA ALADAFPLYP
GIETAGQGYA GI
//
