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Serine hydroxymethyltransferase, cytosolic (SHMT) (EC 2.1.2.1) (Glycine hydroxymethyltransferase) (Serine methylase)

 GLYC_RABIT              Reviewed;         484 AA.
P07511;
01-APR-1988, integrated into UniProtKB/Swiss-Prot.
23-JAN-2007, sequence version 2.
10-OCT-2018, entry version 153.
RecName: Full=Serine hydroxymethyltransferase, cytosolic;
Short=SHMT;
EC=2.1.2.1 {ECO:0000269|PubMed:1381582};
AltName: Full=Glycine hydroxymethyltransferase;
AltName: Full=Serine methylase;
Name=SHMT1;
Oryctolagus cuniculus (Rabbit).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Glires; Lagomorpha; Leporidae;
Oryctolagus.
NCBI_TaxID=9986;
[1]
NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, AND CATALYTIC ACTIVITY.
STRAIN=New Zealand white; TISSUE=Liver;
PubMed=1381582; DOI=10.1042/bj2860117;
Byrne P.C., Sanders P.G., Snell K.;
"Nucleotide sequence and expression of a cDNA encoding rabbit liver
cytosolic serine hydroxymethyltransferase.";
Biochem. J. 286:117-123(1992).
[2]
PROTEIN SEQUENCE OF 2-484, AND ACETYLATION AT ALA-2.
TISSUE=Liver;
PubMed=3553178;
Martini F., Angelaccio S., Pascarella S., Barra D., Bossa F.,
Schirch V.;
"The primary structure of rabbit liver cytosolic serine
hydroxymethyltransferase.";
J. Biol. Chem. 262:5499-5509(1987).
[3]
PROTEIN SEQUENCE OF 2-15, DEAMIDATION AT ASN-6, AND ISOPEPTIDE BOND AT
ASN-6.
PubMed=2318867;
Artigues A., Birkett A., Schirch V.;
"Evidence for the in vivo deamidation and isomerization of an
asparaginyl residue in cytosolic serine hydroxymethyltransferase.";
J. Biol. Chem. 265:4853-4858(1990).
[4]
PROTEIN SEQUENCE OF 194-205, AND ACTIVE SITE CYS-204.
PubMed=7358720;
Schirch L., Slagel S., Barra D., Martini F., Bossa F.;
"Evidence for a sulfhydryl group at the active site of serine
transhydroxymethylase.";
J. Biol. Chem. 255:2986-2989(1980).
[5]
X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL
PHOSPHATE, COFACTOR, AND SUBUNIT.
STRAIN=New Zealand white; TISSUE=Liver;
PubMed=10387080; DOI=10.1021/bi9904151;
Scarsdale J.N., Kazanina G., Radaev S., Schirch V., Wright H.T.;
"Crystal structure of rabbit cytosolic serine hydroxymethyltransferase
at 2.8-A resolution: mechanistic implications.";
Biochemistry 38:8347-8358(1999).
-!- FUNCTION: Interconversion of serine and glycine.
{ECO:0000269|PubMed:1381582}.
-!- CATALYTIC ACTIVITY: 5,10-methylenetetrahydrofolate + glycine +
H(2)O = tetrahydrofolate + L-serine. {ECO:0000269|PubMed:1381582}.
-!- COFACTOR:
Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
Evidence={ECO:0000269|PubMed:10387080};
-!- PATHWAY: One-carbon metabolism; tetrahydrofolate interconversion.
{ECO:0000305}.
-!- SUBUNIT: Homotetramer (PubMed:10387080). Identified in complex
with ABRAXAS2 and the other subunits of the BRISC complex, at
least composed of ABRAXAS2, BRCC3/BRCC36, BABAM2 and BABAM1/NBA1.
{ECO:0000250|UniProtKB:P34896, ECO:0000269|PubMed:10387080}.
-!- SUBCELLULAR LOCATION: Cytoplasm.
-!- PTM: Deamidation of asparagine produces alternatively aspartate or
isoaspartate, which in turn can be converted to aspartate through
carboxylmethylation/demethylation. {ECO:0000269|PubMed:2318867}.
-!- MISCELLANEOUS: In eukaryotes there are two forms of the enzymes: a
cytosolic one and a mitochondrial one. {ECO:0000305}.
-!- SIMILARITY: Belongs to the SHMT family. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; Z11846; CAA77870.1; -; mRNA.
PIR; S24342; XYRBSC.
RefSeq; NP_001095187.1; NM_001101717.1.
UniGene; Ocu.2076; -.
PDB; 1CJ0; X-ray; 2.80 A; A/B=15-484.
PDB; 1LS3; X-ray; 2.70 A; A/B/C/D=2-484.
PDB; 1RV3; X-ray; 2.40 A; A/B=2-484.
PDB; 1RV4; X-ray; 2.95 A; A/B=2-484.
PDB; 1RVU; X-ray; 2.50 A; A/B=2-484.
PDB; 1RVY; X-ray; 2.90 A; A/B=2-484.
PDBsum; 1CJ0; -.
PDBsum; 1LS3; -.
PDBsum; 1RV3; -.
PDBsum; 1RV4; -.
PDBsum; 1RVU; -.
PDBsum; 1RVY; -.
ProteinModelPortal; P07511; -.
SMR; P07511; -.
STRING; 9986.ENSOCUP00000017814; -.
iPTMnet; P07511; -.
PRIDE; P07511; -.
Ensembl; ENSOCUT00000030926; ENSOCUP00000017814; ENSOCUG00000021541.
GeneID; 100009405; -.
KEGG; ocu:100009405; -.
CTD; 6470; -.
eggNOG; KOG2467; Eukaryota.
eggNOG; COG0112; LUCA.
GeneTree; ENSGT00390000002762; -.
HOGENOM; HOG000239405; -.
HOVERGEN; HBG002807; -.
InParanoid; P07511; -.
KO; K00600; -.
OMA; PLEHIIA; -.
OrthoDB; EOG091G05AU; -.
TreeFam; TF314667; -.
BRENDA; 2.1.2.1; 1749.
UniPathway; UPA00193; -.
EvolutionaryTrace; P07511; -.
Proteomes; UP000001811; Unplaced.
Bgee; ENSOCUG00000021541; Expressed in 3 organ(s), highest expression level in liver.
GO; GO:0005829; C:cytosol; ISS:UniProtKB.
GO; GO:0005634; C:nucleus; IEA:Ensembl.
GO; GO:0004372; F:glycine hydroxymethyltransferase activity; ISS:UniProtKB.
GO; GO:0048027; F:mRNA 5'-UTR binding; IEA:Ensembl.
GO; GO:0042803; F:protein homodimerization activity; IEA:Ensembl.
GO; GO:0030170; F:pyridoxal phosphate binding; ISS:UniProtKB.
GO; GO:0070905; F:serine binding; IEA:Ensembl.
GO; GO:0000900; F:translation repressor activity, mRNA regulatory element binding; IEA:Ensembl.
GO; GO:1990830; P:cellular response to leukemia inhibitory factor; IEA:Ensembl.
GO; GO:1904482; P:cellular response to tetrahydrofolate; IEA:Ensembl.
GO; GO:0006231; P:dTMP biosynthetic process; IEA:Ensembl.
GO; GO:0046655; P:folic acid metabolic process; IEA:Ensembl.
GO; GO:0019264; P:glycine biosynthetic process from serine; IEA:InterPro.
GO; GO:0006544; P:glycine metabolic process; ISS:UniProtKB.
GO; GO:0006565; P:L-serine catabolic process; IEA:Ensembl.
GO; GO:0006563; P:L-serine metabolic process; ISS:UniProtKB.
GO; GO:0051289; P:protein homotetramerization; ISS:UniProtKB.
GO; GO:0009113; P:purine nucleobase biosynthetic process; IEA:Ensembl.
GO; GO:0035999; P:tetrahydrofolate interconversion; IEA:UniProtKB-UniPathway.
GO; GO:0046653; P:tetrahydrofolate metabolic process; ISS:UniProtKB.
CDD; cd00378; SHMT; 1.
Gene3D; 3.40.640.10; -; 1.
Gene3D; 3.90.1150.10; -; 2.
HAMAP; MF_00051; SHMT; 1.
InterPro; IPR015424; PyrdxlP-dep_Trfase.
InterPro; IPR015422; PyrdxlP-dep_Trfase_dom1.
InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
InterPro; IPR001085; Ser_HO-MeTrfase.
InterPro; IPR019798; Ser_HO-MeTrfase_PLP_BS.
InterPro; IPR039429; SHMT-like_dom.
PANTHER; PTHR11680; PTHR11680; 1.
Pfam; PF00464; SHMT; 1.
PIRSF; PIRSF000412; SHMT; 1.
SUPFAM; SSF53383; SSF53383; 1.
PROSITE; PS00096; SHMT; 1.
1: Evidence at protein level;
3D-structure; Acetylation; Complete proteome; Cytoplasm;
Direct protein sequencing; Isopeptide bond; One-carbon metabolism;
Pyridoxal phosphate; Reference proteome; Transferase.
INIT_MET 1 1 Removed. {ECO:0000269|PubMed:2318867,
ECO:0000269|PubMed:3553178}.
CHAIN 2 484 Serine hydroxymethyltransferase,
cytosolic.
/FTId=PRO_0000113506.
ACT_SITE 204 204 Nucleophile.
{ECO:0000305|PubMed:7358720}.
ACT_SITE 256 256 Proton donor. {ECO:0000250}.
MOD_RES 2 2 N-acetylalanine.
{ECO:0000269|PubMed:3553178}.
MOD_RES 6 6 Deamidated asparagine; alternate.
{ECO:0000269|PubMed:2318867}.
MOD_RES 257 257 N6-(pyridoxal phosphate)lysine.
{ECO:0000269|PubMed:10387080}.
CROSSLNK 6 7 Isoaspartyl glycine isopeptide (Asn-Gly);
alternate. {ECO:0000269|PubMed:2318867}.
HELIX 18 21 {ECO:0000244|PDB:1RV3}.
STRAND 22 24 {ECO:0000244|PDB:1CJ0}.
HELIX 26 29 {ECO:0000244|PDB:1RV3}.
HELIX 31 45 {ECO:0000244|PDB:1RV3}.
STRAND 46 49 {ECO:0000244|PDB:1RV3}.
HELIX 59 65 {ECO:0000244|PDB:1RV3}.
HELIX 68 70 {ECO:0000244|PDB:1RV3}.
STRAND 80 84 {ECO:0000244|PDB:1RV3}.
HELIX 87 103 {ECO:0000244|PDB:1RV3}.
TURN 108 110 {ECO:0000244|PDB:1RV3}.
STRAND 111 114 {ECO:0000244|PDB:1RV3}.
HELIX 120 131 {ECO:0000244|PDB:1RV3}.
STRAND 137 141 {ECO:0000244|PDB:1RV3}.
HELIX 143 145 {ECO:0000244|PDB:1RV3}.
HELIX 149 151 {ECO:0000244|PDB:1RV3}.
HELIX 162 166 {ECO:0000244|PDB:1RV3}.
STRAND 167 172 {ECO:0000244|PDB:1RV3}.
TURN 176 178 {ECO:0000244|PDB:1RV3}.
STRAND 179 181 {ECO:0000244|PDB:1RV4}.
HELIX 183 193 {ECO:0000244|PDB:1RV3}.
STRAND 196 200 {ECO:0000244|PDB:1RV3}.
HELIX 211 220 {ECO:0000244|PDB:1RV3}.
STRAND 224 228 {ECO:0000244|PDB:1RV3}.
TURN 230 232 {ECO:0000244|PDB:1RV3}.
HELIX 233 238 {ECO:0000244|PDB:1RV3}.
HELIX 244 246 {ECO:0000244|PDB:1RV3}.
STRAND 249 256 {ECO:0000244|PDB:1RV3}.
HELIX 257 259 {ECO:0000244|PDB:1RV3}.
STRAND 265 270 {ECO:0000244|PDB:1RV3}.
HELIX 288 296 {ECO:0000244|PDB:1RV3}.
TURN 297 300 {ECO:0000244|PDB:1RV3}.
HELIX 306 319 {ECO:0000244|PDB:1RV3}.
HELIX 322 344 {ECO:0000244|PDB:1RV3}.
HELIX 350 352 {ECO:0000244|PDB:1RV3}.
STRAND 355 362 {ECO:0000244|PDB:1RV3}.
HELIX 363 366 {ECO:0000244|PDB:1RV3}.
HELIX 370 379 {ECO:0000244|PDB:1RV3}.
STRAND 385 387 {ECO:0000244|PDB:1RV3}.
STRAND 395 397 {ECO:0000244|PDB:1RV4}.
STRAND 400 404 {ECO:0000244|PDB:1RV3}.
HELIX 406 410 {ECO:0000244|PDB:1RV3}.
HELIX 415 437 {ECO:0000244|PDB:1RV3}.
HELIX 445 453 {ECO:0000244|PDB:1RV3}.
HELIX 456 473 {ECO:0000244|PDB:1RV3}.
STRAND 480 482 {ECO:0000244|PDB:1RV3}.
SEQUENCE 484 AA; 52975 MW; C2742A5A8052C5BF CRC64;
MATAVNGAPR DAALWSSHEQ MLAQPLKDSD AEVYDIIKKE SNRQRVGLEL IASENFASRA
VLEALGSCLN NKYSEGYPGQ RYYGGTEHID ELETLCQKRA LQAYGLDPQC WGVNVQPYSG
SPANFAVYTA LVEPHGRIMG LDLPDGGHLT HGFMTDKKKI SATSIFFESM AYKVNPDTGY
IDYDRLEENA RLFHPKLIIA GTSCYSRNLD YGRLRKIADE NGAYLMADMA HISGLVVAGV
VPSPFEHCHV VTTTTHKTLR GCRAGMIFYR RGVRSVDPKT GKEILYNLES LINSAVFPGL
QGGPHNHAIA GVAVALKQAM TPEFKEYQRQ VVANCRALSA ALVELGYKIV TGGSDNHLIL
VDLRSKGTDG GRAEKVLEAC SIACNKNTCP GDKSALRPSG LRLGTPALTS RGLLEKDFQK
VAHFIHRGIE LTVQIQDDTG PRATLKEFKE KLAGDEKHQR AVRALRQEVE SFAALFPLPG
LPGF


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