GenomeNet

Database: UniProt
Entry: D4DTN6_NEIEG
LinkDB: D4DTN6_NEIEG
Original site: D4DTN6_NEIEG 
ID   D4DTN6_NEIEG            Unreviewed;       416 AA.
AC   D4DTN6;
DT   18-MAY-2010, integrated into UniProtKB/TrEMBL.
DT   18-MAY-2010, sequence version 1.
DT   24-JAN-2024, entry version 79.
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   ECO:0000313|EMBL:EFE48851.1};
GN   ORFNames=NEIELOOT_02442 {ECO:0000313|EMBL:EFE48851.1}, NELON_09740
GN   {ECO:0000313|EMBL:AJE19155.1};
OS   Neisseria elongata subsp. glycolytica ATCC 29315.
OC   Bacteria; Pseudomonadota; Betaproteobacteria; Neisseriales; Neisseriaceae;
OC   Neisseria.
OX   NCBI_TaxID=546263 {ECO:0000313|EMBL:EFE48851.1, ECO:0000313|Proteomes:UP000005536};
RN   [1] {ECO:0000313|EMBL:EFE48851.1, ECO:0000313|Proteomes:UP000005536}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 29315 {ECO:0000313|EMBL:EFE48851.1,
RC   ECO:0000313|Proteomes:UP000005536};
RA   Weinstock G., Sodergren E., Clifton S., Fulton L., Fulton B., Courtney L.,
RA   Fronick C., Harrison M., Strong C., Farmer C., Delahaunty K., Markovic C.,
RA   Hall O., Minx P., Tomlinson C., Mitreva M., Nelson J., Hou S., Wollam A.,
RA   Pepin K.H., Johnson M., Bhonagiri V., Zhang X., Suruliraj S., Warren W.,
RA   Chinwalla A., Mardis E.R., Wilson R.K.;
RL   Submitted (FEB-2010) to the EMBL/GenBank/DDBJ databases.
RN   [2] {ECO:0000313|Proteomes:UP000031392}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 29315 {ECO:0000313|Proteomes:UP000031392};
RA   Veyrier F.J., Taha M.-K.;
RT   "Complete Genome sequence of Neisseria elongata subsp. glycolytica.";
RL   Submitted (MAY-2014) to the EMBL/GenBank/DDBJ databases.
RN   [3] {ECO:0000313|EMBL:AJE19155.1, ECO:0000313|Proteomes:UP000031392}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 29315 {ECO:0000313|EMBL:AJE19155.1,
RC   ECO:0000313|Proteomes:UP000031392};
RX   PubMed=26162030;
RA   Veyrier F.J., Biais N., Morales P., Belkacem N., Guilhen C., Ranjeva S.,
RA   Sismeiro O., Pehau-Arnaudet G., Rocha E.P., Werts C., Taha M.K.,
RA   Boneca I.G.;
RT   "Common Cell Shape Evolution of Two Nasopharyngeal Pathogens.";
RL   PLoS Genet. 11:E1005338-E1005338(2015).
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|HAMAP-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}.
CC   ---------------------------------------------------------------------------
CC   Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC   Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC   ---------------------------------------------------------------------------
DR   EMBL; CP007726; AJE19155.1; -; Genomic_DNA.
DR   EMBL; ADBF01000234; EFE48851.1; -; Genomic_DNA.
DR   RefSeq; WP_003774247.1; NZ_CP007726.1.
DR   AlphaFoldDB; D4DTN6; -.
DR   STRING; 546263.NELON_09740; -.
DR   KEGG; nel:NELON_09740; -.
DR   PATRIC; fig|546263.7.peg.2087; -.
DR   HOGENOM; CLU_022477_2_1_4; -.
DR   UniPathway; UPA00193; -.
DR   UniPathway; UPA00288; UER01023.
DR   Proteomes; UP000005536; Unassembled WGS sequence.
DR   Proteomes; UP000031392; 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:SF50; 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:EFE48851.1};
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:UP000031392};
KW   Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000256|HAMAP-
KW   Rule:MF_00051}.
FT   DOMAIN          9..383
FT                   /note="Serine hydroxymethyltransferase-like"
FT                   /evidence="ECO:0000259|Pfam:PF00464"
FT   BINDING         121
FT                   /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT                   /ligand_id="ChEBI:CHEBI:57453"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00051"
FT   BINDING         125..127
FT                   /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT                   /ligand_id="ChEBI:CHEBI:57453"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00051"
FT   SITE            228
FT                   /note="Plays an important role in substrate specificity"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00051"
FT   MOD_RES         229
FT                   /note="N6-(pyridoxal phosphate)lysine"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00051,
FT                   ECO:0000256|PIRSR:PIRSR000412-50"
SQ   SEQUENCE   416 AA;  44800 MW;  F81BC03CB4555B3D CRC64;
     MFSKSVTIAK YDPELAAAIA AEVERQQDHI ELIASENYVS YAVMEAQGSQ LTNKYAEGYP
     NKRYYGGCEH VDVAEQLAID RCKKLFGAEY VNVQPHSGSQ ANQAVYASVL KPGDTILGMS
     LAHGGHLTHG ASVNISGKLY NAVTYGLDEN EVLDYAEVER LALEHKPKMI VAGASAYALQ
     IDWAKFREIA DKVGAYLFVD MAHYAGLIAG GEYPNPVPFA DFVTTTTHKT LRGPRGGVIM
     CRDNTHEKAL NSAIFPSLQG GPLMHVIAAK AVAFKEALQP EFKEYAKQVK INAAAMAEEL
     VKRGLRIISG RTESHVFLVD LRAKNITGKA AEEALGKAHI TINKNAIPND PEKPFVTSGI
     RVGAAAITTR GFSEADAREL ANLVADVLDN PNDEANLSRV AAAAQALCAK NPVYGA
//
DBGET integrated database retrieval system