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Protein

Glycine N-methyltransferase

Gene

GNMT

Organism
Homo sapiens (Human)
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.2 Publications

Catalytic activityi

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei22S-adenosyl-L-methioninePROSITE-ProRule annotation1
Binding sitei31S-adenosyl-L-methioninePROSITE-ProRule annotation1
Binding sitei34SubstratePROSITE-ProRule annotation1
Binding sitei41S-adenosyl-L-methioninePROSITE-ProRule annotation1
Binding sitei65S-adenosyl-L-methionine; via carbonyl oxygenPROSITE-ProRule annotation1
Binding sitei86S-adenosyl-L-methioninePROSITE-ProRule annotation1
Binding sitei139S-adenosyl-L-methionine; via carbonyl oxygenPROSITE-ProRule annotation1
Binding sitei141SubstratePROSITE-ProRule annotation1
Binding sitei178SubstratePROSITE-ProRule annotation1
Binding sitei223SubstratePROSITE-ProRule annotation1

GO - Molecular functioni

  • folic acid binding Source: UniProtKB-KW
  • glycine binding Source: UniProtKB
  • glycine N-methyltransferase activity Source: UniProtKB

GO - Biological processi

  • cellular protein modification process Source: UniProtKB
  • glycogen metabolic process Source: Ensembl
  • glyoxylate metabolic process Source: Reactome
  • methionine metabolic process Source: Ensembl
  • one-carbon metabolic process Source: Ensembl
  • protein homotetramerization Source: UniProtKB
  • regulation of gluconeogenesis Source: Ensembl
  • S-adenosylmethionine metabolic process Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Ligandi

Folate-binding, S-adenosyl-L-methionine

Enzyme and pathway databases

BioCyciZFISH:HS04819-MONOMER.
BRENDAi2.1.1.20. 2681.
ReactomeiR-HSA-2408508. Metabolism of ingested SeMet, Sec, MeSec into H2Se.
R-HSA-389661. Glyoxylate metabolism and glycine degradation.
SABIO-RKQ14749.

Names & Taxonomyi

Protein namesi
Recommended name:
Glycine N-methyltransferase (EC:2.1.1.20)
Gene namesi
Name:GNMT
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 6

Organism-specific databases

HGNCiHGNC:4415. GNMT.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Involvement in diseasei

Glycine N-methyltransferase deficiency (GNMT deficiency)2 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionThe only clinical abnormalities in patients with this deficiency are mild hepatomegaly and chronic elevation of serum transaminases.
See also OMIM:606664
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_01276650L → P in GNMT deficiency; 10% wild-type activity. 2 PublicationsCorresponds to variant rs121907888dbSNPEnsembl.1
Natural variantiVAR_019840141N → S in GNMT deficiency; 0.5% wild-type activity. 2 Publications1
Natural variantiVAR_012767177H → N in GNMT deficiency; 75% wild-type activity, decreases stability of the tetramer. 3 PublicationsCorresponds to variant rs121907889dbSNPEnsembl.1

Keywords - Diseasei

Disease mutation

Organism-specific databases

DisGeNETi27232.
MalaCardsiGNMT.
MIMi606664. phenotype.
OpenTargetsiENSG00000124713.
Orphaneti289891. Hypermethioninemia due to glycine N-methyltransferase deficiency.
PharmGKBiPA28794.

Chemistry databases

DrugBankiDB00145. Glycine.
DB00118. S-Adenosylmethionine.

Polymorphism and mutation databases

BioMutaiGNMT.
DMDMi12644416.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedBy similarity
ChainiPRO_00000875242 – 295Glycine N-methyltransferaseAdd BLAST294

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylvalineBy similarity1
Modified residuei10PhosphoserineBy similarity1
Modified residuei34PhosphotyrosineBy similarity1
Modified residuei46N6-succinyllysineBy similarity1
Modified residuei193N6-succinyllysineBy similarity1
Modified residuei198N6-succinyllysineBy similarity1
Modified residuei203N6-succinyllysineBy similarity1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

PaxDbiQ14749.
PeptideAtlasiQ14749.
PRIDEiQ14749.

PTM databases

iPTMnetiQ14749.
PhosphoSitePlusiQ14749.

Expressioni

Tissue specificityi

Abundant in liver.

Gene expression databases

BgeeiENSG00000124713.
CleanExiHS_GNMT.
ExpressionAtlasiQ14749. baseline and differential.
GenevisibleiQ14749. HS.

Organism-specific databases

HPAiHPA027501.

Interactioni

Subunit structurei

Homotetramer.2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
ARRB1P494077EBI-744239,EBI-743313

Protein-protein interaction databases

BioGridi118081. 19 interactors.
IntActiQ14749. 13 interactors.
MINTiMINT-1436683.
STRINGi9606.ENSP00000361894.

Structurei

Secondary structure

1295
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Turni21 – 24Combined sources4
Helixi28 – 34Combined sources7
Helixi43 – 55Combined sources13
Beta strandi60 – 64Combined sources5
Helixi70 – 78Combined sources9
Beta strandi81 – 87Combined sources7
Helixi89 – 101Combined sources13
Turni102 – 104Combined sources3
Helixi106 – 109Combined sources4
Beta strandi112 – 115Combined sources4
Helixi118 – 120Combined sources3
Helixi121 – 124Combined sources4
Beta strandi133 – 138Combined sources6
Helixi143 – 145Combined sources3
Beta strandi150 – 153Combined sources4
Helixi154 – 165Combined sources12
Beta strandi167 – 178Combined sources12
Helixi180 – 186Combined sources7
Beta strandi195 – 197Combined sources3
Beta strandi204 – 212Combined sources9
Beta strandi215 – 225Combined sources11
Beta strandi239 – 245Combined sources7
Helixi250 – 260Combined sources11
Turni261 – 263Combined sources3
Beta strandi265 – 271Combined sources7
Beta strandi285 – 293Combined sources9

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1R74X-ray2.55A/B2-295[»]
2AZTX-ray2.70A/B1-295[»]
ProteinModelPortaliQ14749.
SMRiQ14749.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ14749.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni117 – 118S-adenosyl-L-methionine bindingPROSITE-ProRule annotation2

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.
InParanoidiQ14749.
KOiK00552.
OMAiMITLDYT.
OrthoDBiEOG091G0J3Z.
PhylomeDBiQ14749.
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.

Q14749-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVDSVYRTRS LGVAAEGLPD QYADGEAARV WQLYIGDTRS RTAEYKAWLL
60 70 80 90 100
GLLRQHGCQR VLDVACGTGV DSIMLVEEGF SVTSVDASDK MLKYALKERW
110 120 130 140 150
NRRHEPAFDK WVIEEANWMT LDKDVPQSAE GGFDAVICLG NSFAHLPDCK
160 170 180 190 200
GDQSEHRLAL KNIASMVRAG GLLVIDHRNY DHILSTGCAP PGKNIYYKSD
210 220 230 240 250
LTKDVTTSVL IVNNKAHMVT LDYTVQVPGA GQDGSPGLSK FRLSYYPHCL
260 270 280 290
ASFTELLQAA FGGKCQHSVL GDFKPYKPGQ TYIPCYFIHV LKRTD
Length:295
Mass (Da):32,742
Last modified:January 23, 2007 - v3
Checksum:i34F4546136FD27ED
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti119Missing in CAA44164 (PubMed:8281755).Curated1
Sequence conflicti129 – 130AE → PK in AAF78289 (PubMed:10843803).Curated2
Sequence conflicti175I → S in CAA44164 (PubMed:8281755).Curated1
Sequence conflicti256 – 260LLQAA → SPSS in CAA44164 (PubMed:8281755).Curated5

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_01276650L → P in GNMT deficiency; 10% wild-type activity. 2 PublicationsCorresponds to variant rs121907888dbSNPEnsembl.1
Natural variantiVAR_019840141N → S in GNMT deficiency; 0.5% wild-type activity. 2 Publications1
Natural variantiVAR_012767177H → N in GNMT deficiency; 75% wild-type activity, decreases stability of the tetramer. 3 PublicationsCorresponds to variant rs121907889dbSNPEnsembl.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF101477 mRNA. Translation: AAF78290.1.
AF101475 Genomic DNA. Translation: AAF78289.1.
AL158815 Genomic DNA. Translation: CAI19462.1.
CH471081 Genomic DNA. Translation: EAX04124.1.
BC032627 mRNA. Translation: AAH32627.1.
X62250 mRNA. Translation: CAA44164.1.
CCDSiCCDS4876.1.
PIRiS42627.
RefSeqiNP_001305794.1. NM_001318865.1.
NP_061833.1. NM_018960.5.
UniGeneiHs.144914.

Genome annotation databases

EnsembliENST00000372808; ENSP00000361894; ENSG00000124713.
GeneIDi27232.
KEGGihsa:27232.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF101477 mRNA. Translation: AAF78290.1.
AF101475 Genomic DNA. Translation: AAF78289.1.
AL158815 Genomic DNA. Translation: CAI19462.1.
CH471081 Genomic DNA. Translation: EAX04124.1.
BC032627 mRNA. Translation: AAH32627.1.
X62250 mRNA. Translation: CAA44164.1.
CCDSiCCDS4876.1.
PIRiS42627.
RefSeqiNP_001305794.1. NM_001318865.1.
NP_061833.1. NM_018960.5.
UniGeneiHs.144914.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1R74X-ray2.55A/B2-295[»]
2AZTX-ray2.70A/B1-295[»]
ProteinModelPortaliQ14749.
SMRiQ14749.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi118081. 19 interactors.
IntActiQ14749. 13 interactors.
MINTiMINT-1436683.
STRINGi9606.ENSP00000361894.

Chemistry databases

DrugBankiDB00145. Glycine.
DB00118. S-Adenosylmethionine.

PTM databases

iPTMnetiQ14749.
PhosphoSitePlusiQ14749.

Polymorphism and mutation databases

BioMutaiGNMT.
DMDMi12644416.

Proteomic databases

PaxDbiQ14749.
PeptideAtlasiQ14749.
PRIDEiQ14749.

Protocols and materials databases

DNASUi27232.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000372808; ENSP00000361894; ENSG00000124713.
GeneIDi27232.
KEGGihsa:27232.

Organism-specific databases

CTDi27232.
DisGeNETi27232.
GeneCardsiGNMT.
HGNCiHGNC:4415. GNMT.
HPAiHPA027501.
MalaCardsiGNMT.
MIMi606628. gene.
606664. phenotype.
neXtProtiNX_Q14749.
OpenTargetsiENSG00000124713.
Orphaneti289891. Hypermethioninemia due to glycine N-methyltransferase deficiency.
PharmGKBiPA28794.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IF1C. Eukaryota.
ENOG410ZWXN. LUCA.
GeneTreeiENSGT00390000006845.
HOGENOMiHOG000276537.
HOVERGENiHBG051748.
InParanoidiQ14749.
KOiK00552.
OMAiMITLDYT.
OrthoDBiEOG091G0J3Z.
PhylomeDBiQ14749.
TreeFamiTF324814.

Enzyme and pathway databases

BioCyciZFISH:HS04819-MONOMER.
BRENDAi2.1.1.20. 2681.
ReactomeiR-HSA-2408508. Metabolism of ingested SeMet, Sec, MeSec into H2Se.
R-HSA-389661. Glyoxylate metabolism and glycine degradation.
SABIO-RKQ14749.

Miscellaneous databases

EvolutionaryTraceiQ14749.
GeneWikiiGNMT.
GenomeRNAii27232.
PROiQ14749.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000124713.
CleanExiHS_GNMT.
ExpressionAtlasiQ14749. baseline and differential.
GenevisibleiQ14749. HS.

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_HUMAN
AccessioniPrimary (citable) accession number: Q14749
Secondary accession number(s): Q5T8W2, Q9NNZ1, Q9NS24
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: January 23, 2007
Last modified: November 30, 2016
This is version 157 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 6
    Human chromosome 6: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. 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.