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Protein

Glycine N-methyltransferase

Gene

Gnmt

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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 activityi

S-adenosyl-L-methionine + glycine = S-adenosyl-L-homocysteine + sarcosine.

Enzyme regulationi

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.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei22S-adenosyl-L-methionine1
Binding sitei31S-adenosyl-L-methionine1
Binding sitei34Substrate1
Binding sitei41S-adenosyl-L-methionine1
Binding sitei65S-adenosyl-L-methionine; via carbonyl oxygen1
Binding sitei86S-adenosyl-L-methionine1
Binding sitei137S-adenosyl-L-methionine; via carbonyl oxygen1
Binding sitei139Substrate1
Binding sitei176Substrate1
Binding sitei221Substrate1

GO - Molecular functioni

  • folic acid binding Source: RGD
  • glycine binding Source: UniProtKB
  • glycine N-methyltransferase activity Source: UniProtKB
  • S-adenosylmethionine-dependent methyltransferase activity Source: RGD
  • selenol Se-methyltransferase activity Source: Reactome

GO - Biological processi

  • folic acid metabolic process Source: RGD
  • glycine metabolic process Source: RGD
  • protein homotetramerization Source: UniProtKB
  • protein tetramerization Source: RGD
  • S-adenosylhomocysteine metabolic process Source: RGD
  • S-adenosylmethionine metabolic process Source: UniProtKB
  • sarcosine metabolic process Source: RGD
  • selenium compound metabolic process Source: Reactome
Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Ligandi

Folate-binding, S-adenosyl-L-methionine

Enzyme and pathway databases

BRENDAi2.1.1.20. 5301.
ReactomeiR-RNO-2408508. Metabolism of ingested SeMet, Sec, MeSec into H2Se.
R-RNO-389661. Glyoxylate metabolism and glycine degradation.
SABIO-RKP13255.

Names & Taxonomyi

Protein namesi
Recommended name:
Glycine N-methyltransferase (EC:2.1.1.20)
Alternative name(s):
Folate-binding protein
Gene namesi
Name:Gnmt
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 9

Organism-specific databases

RGDi2719. Gnmt.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: RGD
  • nucleus Source: RGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi34Y → F: Reduces affinity for glycine. 1 Publication1
Mutagenesisi176R → K: Strongly reduced affinity for glycine. 1 Publication1
Mutagenesisi221Y → F: Reduces affinity for glycine. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00000875282 – 293Glycine N-methyltransferaseAdd BLAST292

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylvaline1 Publication1
Modified residuei10PhosphoserineBy similarity1
Modified residuei34PhosphotyrosineBy similarity1
Modified residuei46N6-succinyllysineBy similarity1
Modified residuei191N6-succinyllysineBy similarity1
Modified residuei196N6-succinyllysineBy similarity1
Modified residuei201N6-succinyllysineBy similarity1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

PaxDbiP13255.
PRIDEiP13255.

PTM databases

iPTMnetiP13255.
PhosphoSitePlusiP13255.

Expressioni

Tissue specificityi

Abundant in liver.

Gene expression databases

BgeeiENSRNOG00000016349.
GenevisibleiP13255. RN.

Interactioni

Subunit structurei

Homotetramer.1 Publication

Protein-protein interaction databases

MINTiMINT-4567246.
STRINGi10116.ENSRNOP00000022307.

Structurei

Secondary structure

1293
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi5 – 9Combined sources5
Beta strandi11 – 13Combined sources3
Turni21 – 24Combined sources4
Helixi26 – 35Combined sources10
Beta strandi39 – 41Combined sources3
Helixi43 – 55Combined sources13
Beta strandi60 – 63Combined sources4
Helixi70 – 77Combined sources8
Beta strandi81 – 87Combined sources7
Helixi89 – 101Combined sources13
Turni102 – 104Combined sources3
Helixi106 – 109Combined sources4
Beta strandi112 – 115Combined sources4
Helixi118 – 120Combined sources3
Helixi121 – 124Combined sources4
Beta strandi131 – 136Combined sources6
Turni137 – 139Combined sources3
Helixi141 – 143Combined sources3
Beta strandi147 – 151Combined sources5
Helixi152 – 163Combined sources12
Beta strandi165 – 176Combined sources12
Helixi178 – 184Combined sources7
Beta strandi193 – 195Combined sources3
Beta strandi202 – 210Combined sources9
Beta strandi213 – 225Combined sources13
Beta strandi229 – 232Combined sources4
Beta strandi235 – 243Combined sources9
Helixi248 – 257Combined sources10
Turni258 – 261Combined sources4
Beta strandi263 – 269Combined sources7
Beta strandi283 – 291Combined sources9

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1BHJX-ray2.50A/B2-293[»]
1D2CX-ray2.50A/B2-293[»]
1D2GX-ray2.50A/B2-293[»]
1D2HX-ray3.00A/B/C/D2-293[»]
1KIAX-ray2.80A/B/C/D2-293[»]
1NBHX-ray2.80A/B/C/D2-293[»]
1NBIX-ray3.00A/B/C/D2-293[»]
1XVAX-ray2.20A/B2-293[»]
2IDJX-ray2.35A/B/C/D2-293[»]
2IDKX-ray2.55A/B/C/D2-293[»]
3THRX-ray2.00A/B/C/D2-293[»]
3THSX-ray2.50A/B/C/D2-293[»]
DisProtiDP00031.
ProteinModelPortaliP13255.
SMRiP13255.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP13255.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni117 – 118S-adenosyl-L-methionine binding2

Sequence similaritiesi

Belongs to the class I-like SAM-binding methyltransferase superfamily. Glycine N-methyltransferase family.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiENOG410IF1C. Eukaryota.
ENOG410ZWXN. LUCA.
GeneTreeiENSGT00390000006845.
HOGENOMiHOG000276537.
HOVERGENiHBG051748.
InParanoidiP13255.
KOiK00552.
OMAiMITLDYT.
OrthoDBiEOG091G0J3Z.
PhylomeDBiP13255.
TreeFamiTF324814.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
InterProiIPR014369. Gly/Sar_N_MeTrfase.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PANTHERiPTHR16458. PTHR16458. 1 hit.
PIRSFiPIRSF000385. Gly_N-mtase. 1 hit.
SUPFAMiSSF53335. SSF53335. 1 hit.
PROSITEiPS51600. SAM_GNMT. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P13255-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVDSVYRTRS LGVAAEGIPD QYADGEAARV WQLYIGDTRS RTAEYKAWLL
60 70 80 90 100
GLLRQHGCHR VLDVACGTGV DSIMLVEEGF SVTSVDASDK MLKYALKERW
110 120 130 140 150
NRRKEPAFDK WVIEEANWLT LDKDVPAGDG FDAVICLGNS FAHLPDSKGD
160 170 180 190 200
QSEHRLALKN IASMVRPGGL LVIDHRNYDY ILSTGCAPPG KNIYYKSDLT
210 220 230 240 250
KDITTSVLTV NNKAHMVTLD YTVQVPGAGR DGAPGFSKFR LSYYPHCLAS
260 270 280 290
FTELVQEAFG GRCQHSVLGD FKPYRPGQAY VPCYFIHVLK KTG
Length:293
Mass (Da):32,549
Last modified:January 23, 2007 - v2
Checksum:i4E98C7512F0228A5
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X06150 mRNA. Translation: CAA29508.1.
X07833 Genomic DNA. Translation: CAA30686.1.
PIRiS00112.
RefSeqiNP_058780.1. NM_017084.1.
UniGeneiRn.11142.

Genome annotation databases

EnsembliENSRNOT00000022307; ENSRNOP00000022307; ENSRNOG00000016349.
GeneIDi25134.
KEGGirno:25134.
UCSCiRGD:2719. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X06150 mRNA. Translation: CAA29508.1.
X07833 Genomic DNA. Translation: CAA30686.1.
PIRiS00112.
RefSeqiNP_058780.1. NM_017084.1.
UniGeneiRn.11142.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1BHJX-ray2.50A/B2-293[»]
1D2CX-ray2.50A/B2-293[»]
1D2GX-ray2.50A/B2-293[»]
1D2HX-ray3.00A/B/C/D2-293[»]
1KIAX-ray2.80A/B/C/D2-293[»]
1NBHX-ray2.80A/B/C/D2-293[»]
1NBIX-ray3.00A/B/C/D2-293[»]
1XVAX-ray2.20A/B2-293[»]
2IDJX-ray2.35A/B/C/D2-293[»]
2IDKX-ray2.55A/B/C/D2-293[»]
3THRX-ray2.00A/B/C/D2-293[»]
3THSX-ray2.50A/B/C/D2-293[»]
DisProtiDP00031.
ProteinModelPortaliP13255.
SMRiP13255.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

MINTiMINT-4567246.
STRINGi10116.ENSRNOP00000022307.

PTM databases

iPTMnetiP13255.
PhosphoSitePlusiP13255.

Proteomic databases

PaxDbiP13255.
PRIDEiP13255.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000022307; ENSRNOP00000022307; ENSRNOG00000016349.
GeneIDi25134.
KEGGirno:25134.
UCSCiRGD:2719. rat.

Organism-specific databases

CTDi27232.
RGDi2719. Gnmt.

Phylogenomic databases

eggNOGiENOG410IF1C. Eukaryota.
ENOG410ZWXN. LUCA.
GeneTreeiENSGT00390000006845.
HOGENOMiHOG000276537.
HOVERGENiHBG051748.
InParanoidiP13255.
KOiK00552.
OMAiMITLDYT.
OrthoDBiEOG091G0J3Z.
PhylomeDBiP13255.
TreeFamiTF324814.

Enzyme and pathway databases

BRENDAi2.1.1.20. 5301.
ReactomeiR-RNO-2408508. Metabolism of ingested SeMet, Sec, MeSec into H2Se.
R-RNO-389661. Glyoxylate metabolism and glycine degradation.
SABIO-RKP13255.

Miscellaneous databases

EvolutionaryTraceiP13255.
PROiP13255.

Gene expression databases

BgeeiENSRNOG00000016349.
GenevisibleiP13255. RN.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
InterProiIPR014369. Gly/Sar_N_MeTrfase.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PANTHERiPTHR16458. PTHR16458. 1 hit.
PIRSFiPIRSF000385. Gly_N-mtase. 1 hit.
SUPFAMiSSF53335. SSF53335. 1 hit.
PROSITEiPS51600. SAM_GNMT. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiGNMT_RAT
AccessioniPrimary (citable) accession number: P13255
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 1, 1990
Last sequence update: January 23, 2007
Last modified: November 2, 2016
This is version 144 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.