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Glycine N-methyltransferase (EC 2.1.1.20) (Folate-binding protein)

 GNMT_RAT                Reviewed;         293 AA.
P13255;
01-JAN-1990, integrated into UniProtKB/Swiss-Prot.
23-JAN-2007, sequence version 2.
22-NOV-2017, entry version 149.
RecName: Full=Glycine N-methyltransferase;
EC=2.1.1.20;
AltName: Full=Folate-binding protein;
Name=Gnmt;
Rattus norvegicus (Rat).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
Muroidea; Muridae; Murinae; Rattus.
NCBI_TaxID=10116;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA], PROTEIN SEQUENCE OF 2-7,
CLEAVAGE OF INITIATOR METHIONINE, AND ACETYLATION AT VAL-2.
STRAIN=Sprague-Dawley;
PubMed=2822402; DOI=10.1111/j.1432-1033.1987.tb13398.x;
Ogawa H., Konishi K., Takata Y., Nakashima H., Fujioka M.;
"Rat glycine methyltransferase. Complete amino acid sequence deduced
from a cDNA clone and characterization of the genomic DNA.";
Eur. J. Biochem. 168:141-151(1987).
[2]
X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
TISSUE=Liver;
PubMed=8810903; DOI=10.1021/bi961068n;
Fu Z., Hu Y., Konishi K., Takata Y., Ogawa H., Gomi T., Fujioka M.,
Takusagawa F.;
"Crystal structure of glycine N-methyltransferase from rat liver.";
Biochemistry 35:11985-11993(1996).
[3]
X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
PubMed=9655336; DOI=10.1002/pro.5560070608;
Pattanayek R., Newcomer M.E., Wagner C.;
"Crystal structure of apo-glycine N-methyltransferase (GNMT).";
Protein Sci. 7:1326-1331(1998).
[4]
X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
PubMed=10756111; DOI=10.1006/jmbi.2000.3637;
Huang Y., Komoto J., Konishi K., Takata Y., Ogawa H., Gomi T.,
Fujioka M., Takusagawa F.;
"Mechanisms for auto-inhibition and forced product release in glycine
N-methyltransferase: crystal structures of wild-type, mutant R175K and
S-adenosylhomocysteine-bound R175K enzymes.";
J. Mol. Biol. 298:149-162(2000).
[5]
X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 2-292 IN COMPLEXES WITH
S-ADENOSYL-L-METHIONINE AND ACETATE, AND MUTAGENESIS OF TYR-34;
ARG-176 AND TYR-221.
PubMed=12859184; DOI=10.1021/bi034245a;
Takata Y., Huang Y., Komoto J., Yamada T., Konishi K., Ogawa H.,
Gomi T., Fujioka M., Takusagawa F.;
"Catalytic mechanism of glycine N-methyltransferase.";
Biochemistry 42:8394-8402(2003).
[6]
X-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS) OF 2-292 IN COMPLEX WITH
5-METHYLTETRAHYDROFOLATE, AND ENZYME REGULATION.
PubMed=17158459; DOI=10.1074/jbc.M610384200;
Luka Z., Pakhomova S., Loukachevitch L.V., Egli M., Newcomer M.E.,
Wagner C.;
"5-methyltetrahydrofolate is bound in intersubunit areas of rat liver
folate-binding protein glycine N-methyltransferase.";
J. Biol. Chem. 282:4069-4075(2007).
-!- FUNCTION: Catalyzes the methylation of glycine by using S-
adenosylmethionine (AdoMet) to form N-methylglycine (sarcosine)
with the concomitant production of S-adenosylhomocysteine
(AdoHcy). Possible crucial role in the regulation of tissue
concentration of AdoMet and of metabolism of methionine.
-!- CATALYTIC ACTIVITY: S-adenosyl-L-methionine + glycine = S-
adenosyl-L-homocysteine + sarcosine.
-!- ENZYME REGULATION: Inhibited by 5-methyltetrahydrofolate
pentaglutamate. Two molecules of 5-methyltetrahydrofolate are
bound per tetramer. The binding sites are localized between
subunits. Inhibitor binding may preclude movements of the
polypeptide chain that are necessary for enzyme activity.
{ECO:0000269|PubMed:17158459}.
-!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:17158459}.
-!- SUBCELLULAR LOCATION: Cytoplasm.
-!- TISSUE SPECIFICITY: Abundant in liver.
-!- SIMILARITY: Belongs to the class I-like SAM-binding
methyltransferase superfamily. Glycine N-methyltransferase family.
{ECO:0000255|PROSITE-ProRule:PRU00932}.
-----------------------------------------------------------------------
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EMBL; X06150; CAA29508.1; -; mRNA.
EMBL; X07833; CAA30686.1; -; Genomic_DNA.
PIR; S00112; S00112.
RefSeq; NP_058780.1; NM_017084.1.
UniGene; Rn.11142; -.
PDB; 1BHJ; X-ray; 2.50 A; A/B=2-293.
PDB; 1D2C; X-ray; 2.50 A; A/B=2-293.
PDB; 1D2G; X-ray; 2.50 A; A/B=2-293.
PDB; 1D2H; X-ray; 3.00 A; A/B/C/D=2-293.
PDB; 1KIA; X-ray; 2.80 A; A/B/C/D=2-293.
PDB; 1NBH; X-ray; 2.80 A; A/B/C/D=2-293.
PDB; 1NBI; X-ray; 3.00 A; A/B/C/D=2-293.
PDB; 1XVA; X-ray; 2.20 A; A/B=2-293.
PDB; 2IDJ; X-ray; 2.35 A; A/B/C/D=2-293.
PDB; 2IDK; X-ray; 2.55 A; A/B/C/D=2-293.
PDB; 3THR; X-ray; 2.00 A; A/B/C/D=2-293.
PDB; 3THS; X-ray; 2.50 A; A/B/C/D=2-293.
PDBsum; 1BHJ; -.
PDBsum; 1D2C; -.
PDBsum; 1D2G; -.
PDBsum; 1D2H; -.
PDBsum; 1KIA; -.
PDBsum; 1NBH; -.
PDBsum; 1NBI; -.
PDBsum; 1XVA; -.
PDBsum; 2IDJ; -.
PDBsum; 2IDK; -.
PDBsum; 3THR; -.
PDBsum; 3THS; -.
DisProt; DP00031; -.
ProteinModelPortal; P13255; -.
SMR; P13255; -.
MINT; MINT-4567246; -.
STRING; 10116.ENSRNOP00000022307; -.
iPTMnet; P13255; -.
PhosphoSitePlus; P13255; -.
PaxDb; P13255; -.
PRIDE; P13255; -.
Ensembl; ENSRNOT00000022307; ENSRNOP00000022307; ENSRNOG00000016349.
GeneID; 25134; -.
KEGG; rno:25134; -.
UCSC; RGD:2719; rat.
CTD; 27232; -.
RGD; 2719; Gnmt.
eggNOG; ENOG410IF1C; Eukaryota.
eggNOG; ENOG410ZWXN; LUCA.
GeneTree; ENSGT00390000006845; -.
HOGENOM; HOG000276537; -.
HOVERGEN; HBG051748; -.
InParanoid; P13255; -.
KO; K00552; -.
OMA; QAYIPCY; -.
OrthoDB; EOG091G0J3Z; -.
PhylomeDB; P13255; -.
TreeFam; TF324814; -.
BRENDA; 2.1.1.20; 5301.
Reactome; R-RNO-389661; Glyoxylate metabolism and glycine degradation.
SABIO-RK; P13255; -.
EvolutionaryTrace; P13255; -.
PRO; PR:P13255; -.
Proteomes; UP000002494; Chromosome 9.
Bgee; ENSRNOG00000016349; -.
Genevisible; P13255; RN.
GO; GO:0005829; C:cytosol; IDA:RGD.
GO; GO:0034708; C:methyltransferase complex; IMP:CAFA.
GO; GO:0005634; C:nucleus; IDA:RGD.
GO; GO:0005542; F:folic acid binding; IDA:RGD.
GO; GO:0016594; F:glycine binding; IDA:UniProtKB.
GO; GO:0017174; F:glycine N-methyltransferase activity; IDA:UniProtKB.
GO; GO:0042802; F:identical protein binding; IMP:CAFA.
GO; GO:1904047; F:S-adenosyl-L-methionine binding; IMP:CAFA.
GO; GO:0008757; F:S-adenosylmethionine-dependent methyltransferase activity; IDA:RGD.
GO; GO:0098603; F:selenol Se-methyltransferase activity; TAS:Reactome.
GO; GO:0046655; P:folic acid metabolic process; TAS:RGD.
GO; GO:0006544; P:glycine metabolic process; IMP:CAFA.
GO; GO:0005977; P:glycogen metabolic process; ISO:RGD.
GO; GO:0006555; P:methionine metabolic process; ISO:RGD.
GO; GO:0032259; P:methylation; IMP:CAFA.
GO; GO:0006730; P:one-carbon metabolic process; ISO:RGD.
GO; GO:0051289; P:protein homotetramerization; IMP:CAFA.
GO; GO:0051262; P:protein tetramerization; IDA:RGD.
GO; GO:0006111; P:regulation of gluconeogenesis; ISO:RGD.
GO; GO:0046498; P:S-adenosylhomocysteine metabolic process; IDA:RGD.
GO; GO:0046500; P:S-adenosylmethionine metabolic process; IDA:UniProtKB.
GO; GO:1901052; P:sarcosine metabolic process; IMP:RGD.
GO; GO:0001887; P:selenium compound metabolic process; TAS:Reactome.
InterPro; IPR014369; Gly/Sar_N_MeTrfase.
InterPro; IPR029063; SAM-dependent_MTases.
PANTHER; PTHR16458; PTHR16458; 1.
PIRSF; PIRSF000385; Gly_N-mtase; 1.
SUPFAM; SSF53335; SSF53335; 1.
PROSITE; PS51600; SAM_GNMT; 1.
1: Evidence at protein level;
3D-structure; Acetylation; Complete proteome; Cytoplasm;
Direct protein sequencing; Folate-binding; Methyltransferase;
Phosphoprotein; Reference proteome; S-adenosyl-L-methionine;
Transferase.
INIT_MET 1 1 Removed. {ECO:0000269|PubMed:2822402}.
CHAIN 2 293 Glycine N-methyltransferase.
/FTId=PRO_0000087528.
REGION 117 118 S-adenosyl-L-methionine binding.
BINDING 22 22 S-adenosyl-L-methionine.
BINDING 31 31 S-adenosyl-L-methionine.
BINDING 34 34 Substrate.
BINDING 41 41 S-adenosyl-L-methionine.
BINDING 65 65 S-adenosyl-L-methionine; via carbonyl
oxygen.
BINDING 86 86 S-adenosyl-L-methionine.
BINDING 137 137 S-adenosyl-L-methionine; via carbonyl
oxygen.
BINDING 139 139 Substrate.
BINDING 176 176 Substrate.
BINDING 221 221 Substrate.
MOD_RES 2 2 N-acetylvaline.
{ECO:0000269|PubMed:2822402}.
MOD_RES 10 10 Phosphoserine.
{ECO:0000250|UniProtKB:Q9QXF8}.
MOD_RES 34 34 Phosphotyrosine.
{ECO:0000250|UniProtKB:Q9QXF8}.
MOD_RES 46 46 N6-succinyllysine.
{ECO:0000250|UniProtKB:Q9QXF8}.
MOD_RES 191 191 N6-succinyllysine.
{ECO:0000250|UniProtKB:Q9QXF8}.
MOD_RES 196 196 N6-succinyllysine.
{ECO:0000250|UniProtKB:Q9QXF8}.
MOD_RES 201 201 N6-succinyllysine.
{ECO:0000250|UniProtKB:Q9QXF8}.
MUTAGEN 34 34 Y->F: Reduces affinity for glycine.
{ECO:0000269|PubMed:12859184}.
MUTAGEN 176 176 R->K: Strongly reduced affinity for
glycine. {ECO:0000269|PubMed:12859184}.
MUTAGEN 221 221 Y->F: Reduces affinity for glycine.
{ECO:0000269|PubMed:12859184}.
STRAND 5 9 {ECO:0000244|PDB:3THR}.
STRAND 11 13 {ECO:0000244|PDB:1NBH}.
TURN 21 24 {ECO:0000244|PDB:3THR}.
HELIX 26 35 {ECO:0000244|PDB:3THR}.
STRAND 39 41 {ECO:0000244|PDB:2IDJ}.
HELIX 43 55 {ECO:0000244|PDB:3THR}.
STRAND 60 63 {ECO:0000244|PDB:3THR}.
HELIX 70 77 {ECO:0000244|PDB:3THR}.
STRAND 81 87 {ECO:0000244|PDB:3THR}.
HELIX 89 101 {ECO:0000244|PDB:3THR}.
TURN 102 104 {ECO:0000244|PDB:3THR}.
HELIX 106 109 {ECO:0000244|PDB:3THR}.
STRAND 112 115 {ECO:0000244|PDB:3THR}.
HELIX 118 120 {ECO:0000244|PDB:3THR}.
HELIX 121 124 {ECO:0000244|PDB:3THR}.
STRAND 131 136 {ECO:0000244|PDB:3THR}.
TURN 137 139 {ECO:0000244|PDB:1NBH}.
HELIX 141 143 {ECO:0000244|PDB:3THR}.
STRAND 147 151 {ECO:0000244|PDB:3THR}.
HELIX 152 163 {ECO:0000244|PDB:3THR}.
STRAND 165 176 {ECO:0000244|PDB:3THR}.
HELIX 178 184 {ECO:0000244|PDB:3THR}.
STRAND 193 195 {ECO:0000244|PDB:3THR}.
STRAND 202 210 {ECO:0000244|PDB:3THR}.
STRAND 213 225 {ECO:0000244|PDB:3THR}.
STRAND 229 232 {ECO:0000244|PDB:1XVA}.
STRAND 235 243 {ECO:0000244|PDB:3THR}.
HELIX 248 257 {ECO:0000244|PDB:3THR}.
TURN 258 261 {ECO:0000244|PDB:3THR}.
STRAND 263 269 {ECO:0000244|PDB:3THR}.
STRAND 283 291 {ECO:0000244|PDB:3THR}.
SEQUENCE 293 AA; 32549 MW; 4E98C7512F0228A5 CRC64;
MVDSVYRTRS LGVAAEGIPD QYADGEAARV WQLYIGDTRS RTAEYKAWLL GLLRQHGCHR
VLDVACGTGV DSIMLVEEGF SVTSVDASDK MLKYALKERW NRRKEPAFDK WVIEEANWLT
LDKDVPAGDG FDAVICLGNS FAHLPDSKGD QSEHRLALKN IASMVRPGGL LVIDHRNYDY
ILSTGCAPPG KNIYYKSDLT KDITTSVLTV NNKAHMVTLD YTVQVPGAGR DGAPGFSKFR
LSYYPHCLAS FTELVQEAFG GRCQHSVLGD FKPYRPGQAY VPCYFIHVLK KTG


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