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Q14749

- GNMT_HUMAN

UniProt

Q14749 - GNMT_HUMAN

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Protein
Glycine N-methyltransferase
Gene
GNMT
Organism
Homo sapiens (Human)
Status
Reviewed - 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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei22 – 221S-adenosyl-L-methionine By similarity
Binding sitei31 – 311S-adenosyl-L-methionine By similarity
Binding sitei34 – 341Substrate By similarity
Binding sitei41 – 411S-adenosyl-L-methionine By similarity
Binding sitei65 – 651S-adenosyl-L-methionine; via carbonyl oxygen By similarity
Binding sitei86 – 861S-adenosyl-L-methionine By similarity
Binding sitei139 – 1391S-adenosyl-L-methionine; via carbonyl oxygen By similarity
Binding sitei141 – 1411Substrate By similarity
Binding sitei178 – 1781Substrate By similarity
Binding sitei223 – 2231Substrate By similarity

GO - Molecular functioni

  1. folic acid binding Source: UniProtKB-KW
  2. glycine N-methyltransferase activity Source: UniProtKB
  3. glycine binding Source: UniProtKB
  4. protein binding Source: IntAct

GO - Biological processi

  1. S-adenosylmethionine metabolic process Source: UniProtKB
  2. cellular protein modification process Source: UniProtKB
  3. glycogen metabolic process Source: Ensembl
  4. methionine metabolic process Source: Ensembl
  5. one-carbon metabolic process Source: Ensembl
  6. protein homotetramerization Source: UniProtKB
  7. regulation of gluconeogenesis Source: Ensembl
Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Ligandi

Folate-binding, S-adenosyl-L-methionine

Enzyme and pathway databases

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
ProteomesiUP000005640: Chromosome 6

Organism-specific databases

HGNCiHGNC:4415. GNMT.

Subcellular locationi

GO - Cellular componenti

  1. cytoplasm Source: HPA
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Involvement in diseasei

Glycine N-methyltransferase deficiency (GNMT deficiency) [MIM:606664]: The only clinical abnormalities in patients with this deficiency are mild hepatomegaly and chronic elevation of serum transaminases.
Note: The disease is caused by mutations affecting the gene represented in this entry.
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti50 – 501L → P in GNMT deficiency; 10% wild-type activity. 2 Publications
VAR_012766
Natural varianti141 – 1411N → S in GNMT deficiency; 0.5% wild-type activity. 2 Publications
VAR_019840
Natural varianti177 – 1771H → N in GNMT deficiency; 75% wild-type activity, decreases stability of the tetramer. 3 Publications
VAR_012767

Keywords - Diseasei

Disease mutation

Organism-specific databases

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

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed By similarity
Chaini2 – 295294Glycine N-methyltransferase
PRO_0000087524Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylvaline By similarity
Modified residuei10 – 101Phosphoserine By similarity
Modified residuei46 – 461N6-succinyllysine By similarity
Modified residuei193 – 1931N6-succinyllysine By similarity
Modified residuei198 – 1981N6-succinyllysine By similarity
Modified residuei203 – 2031N6-succinyllysine By similarity

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

PaxDbiQ14749.
PRIDEiQ14749.

PTM databases

PhosphoSiteiQ14749.

Expressioni

Tissue specificityi

Abundant in liver.

Gene expression databases

BgeeiQ14749.
CleanExiHS_GNMT.
GenevestigatoriQ14749.

Organism-specific databases

HPAiHPA027501.

Interactioni

Subunit structurei

Homotetramer.2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
ARRB1P494075EBI-744239,EBI-743313

Protein-protein interaction databases

BioGridi118081. 12 interactions.
IntActiQ14749. 7 interactions.
MINTiMINT-1436683.
STRINGi9606.ENSP00000361894.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni21 – 244
Helixi28 – 347
Helixi43 – 5513
Beta strandi60 – 645
Helixi70 – 789
Beta strandi81 – 877
Helixi89 – 10113
Turni102 – 1043
Helixi106 – 1094
Beta strandi112 – 1154
Helixi118 – 1203
Helixi121 – 1244
Beta strandi133 – 1386
Helixi143 – 1453
Beta strandi150 – 1534
Helixi154 – 16512
Beta strandi167 – 17812
Helixi180 – 1867
Beta strandi195 – 1973
Beta strandi204 – 2129
Beta strandi215 – 22511
Beta strandi239 – 2457
Helixi250 – 26011
Turni261 – 2633
Beta strandi265 – 2717
Beta strandi285 – 2939

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1R74X-ray2.55A/B2-295[»]
2AZTX-ray2.70A/B1-295[»]
ProteinModelPortaliQ14749.
SMRiQ14749. Positions 6-294.

Miscellaneous databases

EvolutionaryTraceiQ14749.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni117 – 1182S-adenosyl-L-methionine binding By similarity

Sequence similaritiesi

Phylogenomic databases

eggNOGiNOG78825.
HOGENOMiHOG000276537.
HOVERGENiHBG051748.
InParanoidiQ14749.
KOiK00552.
OMAiLIIDHRN.
OrthoDBiEOG76QFHR.
PhylomeDBiQ14749.
TreeFamiTF324814.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
InterProiIPR014369. Gly/Sar_N_MeTrfase.
IPR029063. SAM-dependent_MTases-like.
[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

MVDSVYRTRS LGVAAEGLPD QYADGEAARV WQLYIGDTRS RTAEYKAWLL    50
GLLRQHGCQR VLDVACGTGV DSIMLVEEGF SVTSVDASDK MLKYALKERW 100
NRRHEPAFDK WVIEEANWMT LDKDVPQSAE GGFDAVICLG NSFAHLPDCK 150
GDQSEHRLAL KNIASMVRAG GLLVIDHRNY DHILSTGCAP PGKNIYYKSD 200
LTKDVTTSVL IVNNKAHMVT LDYTVQVPGA GQDGSPGLSK FRLSYYPHCL 250
ASFTELLQAA FGGKCQHSVL GDFKPYKPGQ TYIPCYFIHV LKRTD 295
Length:295
Mass (Da):32,742
Last modified:January 23, 2007 - v3
Checksum:i34F4546136FD27ED
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti50 – 501L → P in GNMT deficiency; 10% wild-type activity. 2 Publications
VAR_012766
Natural varianti141 – 1411N → S in GNMT deficiency; 0.5% wild-type activity. 2 Publications
VAR_019840
Natural varianti177 – 1771H → N in GNMT deficiency; 75% wild-type activity, decreases stability of the tetramer. 3 Publications
VAR_012767

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti119 – 1191Missing in CAA44164. 1 Publication
Sequence conflicti129 – 1302AE → PK in AAF78289. 1 Publication
Sequence conflicti175 – 1751I → S in CAA44164. 1 Publication
Sequence conflicti256 – 2605LLQAA → SPSS in CAA44164. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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_061833.1. NM_018960.4.
UniGeneiHs.144914.

Genome annotation databases

EnsembliENST00000372808; ENSP00000361894; ENSG00000124713.
GeneIDi27232.
KEGGihsa:27232.
UCSCiuc003otd.3. human.

Polymorphism databases

DMDMi12644416.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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 .
CCDSi CCDS4876.1.
PIRi S42627.
RefSeqi NP_061833.1. NM_018960.4.
UniGenei Hs.144914.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1R74 X-ray 2.55 A/B 2-295 [» ]
2AZT X-ray 2.70 A/B 1-295 [» ]
ProteinModelPortali Q14749.
SMRi Q14749. Positions 6-294.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 118081. 12 interactions.
IntActi Q14749. 7 interactions.
MINTi MINT-1436683.
STRINGi 9606.ENSP00000361894.

Chemistry

DrugBanki DB00145. Glycine.
DB00118. S-Adenosylmethionine.

PTM databases

PhosphoSitei Q14749.

Polymorphism databases

DMDMi 12644416.

Proteomic databases

PaxDbi Q14749.
PRIDEi Q14749.

Protocols and materials databases

DNASUi 27232.
Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000372808 ; ENSP00000361894 ; ENSG00000124713 .
GeneIDi 27232.
KEGGi hsa:27232.
UCSCi uc003otd.3. human.

Organism-specific databases

CTDi 27232.
GeneCardsi GC06P042928.
HGNCi HGNC:4415. GNMT.
HPAi HPA027501.
MIMi 606628. gene.
606664. phenotype.
neXtProti NX_Q14749.
Orphaneti 289891. Hypermethioninemia due to glycine N-methyltransferase deficiency.
PharmGKBi PA28794.
GenAtlasi Search...

Phylogenomic databases

eggNOGi NOG78825.
HOGENOMi HOG000276537.
HOVERGENi HBG051748.
InParanoidi Q14749.
KOi K00552.
OMAi LIIDHRN.
OrthoDBi EOG76QFHR.
PhylomeDBi Q14749.
TreeFami TF324814.

Enzyme and pathway databases

SABIO-RK Q14749.

Miscellaneous databases

EvolutionaryTracei Q14749.
GeneWikii GNMT.
GenomeRNAii 27232.
NextBioi 50091.
PROi Q14749.
SOURCEi Search...

Gene expression databases

Bgeei Q14749.
CleanExi HS_GNMT.
Genevestigatori Q14749.

Family and domain databases

Gene3Di 3.40.50.150. 1 hit.
InterProi IPR014369. Gly/Sar_N_MeTrfase.
IPR029063. SAM-dependent_MTases-like.
[Graphical view ]
PANTHERi PTHR16458. PTHR16458. 1 hit.
PIRSFi PIRSF000385. Gly_N-mtase. 1 hit.
SUPFAMi SSF53335. SSF53335. 1 hit.
PROSITEi PS51600. SAM_GNMT. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Characterization of glycine-N-methyltransferase-gene expression in human hepatocellular carcinoma."
    Chen Y.-M.A., Shiu J.Y., Tzeng S.J., Shih L.S., Chen Y.J., Lui W.Y., Chen P.H.
    Int. J. Cancer 75:787-793(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  2. "Genomic structure, expression, and chromosomal localization of the human glycine N-methyltransferase gene."
    Chen Y.-M.A., Chen L.-Y., Wong F.H., Lee C.M., Chang T.J., Yang-Feng T.L.
    Genomics 66:43-47(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Tissue: Placenta.
  3. "The DNA sequence and analysis of human chromosome 6."
    Mungall A.J., Palmer S.A., Sims S.K., Edwards C.A., Ashurst J.L., Wilming L., Jones M.C., Horton R., Hunt S.E., Scott C.E., Gilbert J.G.R., Clamp M.E., Bethel G., Milne S., Ainscough R., Almeida J.P., Ambrose K.D., Andrews T.D.
    , Ashwell R.I.S., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beare D.M., Beasley H., Beasley O., Bird C.P., Blakey S.E., Bray-Allen S., Brook J., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Clark S.Y., Clark G., Clee C.M., Clegg S., Cobley V., Collier R.E., Collins J.E., Colman L.K., Corby N.R., Coville G.J., Culley K.M., Dhami P., Davies J., Dunn M., Earthrowl M.E., Ellington A.E., Evans K.A., Faulkner L., Francis M.D., Frankish A., Frankland J., French L., Garner P., Garnett J., Ghori M.J., Gilby L.M., Gillson C.J., Glithero R.J., Grafham D.V., Grant M., Gribble S., Griffiths C., Griffiths M.N.D., Hall R., Halls K.S., Hammond S., Harley J.L., Hart E.A., Heath P.D., Heathcott R., Holmes S.J., Howden P.J., Howe K.L., Howell G.R., Huckle E., Humphray S.J., Humphries M.D., Hunt A.R., Johnson C.M., Joy A.A., Kay M., Keenan S.J., Kimberley A.M., King A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C.R., Lloyd D.M., Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M., Maslen G.L., Matthews L., McCann O.T., McLaren S.J., McLay K., McMurray A., Moore M.J.F., Mullikin J.C., Niblett D., Nickerson T., Novik K.L., Oliver K., Overton-Larty E.K., Parker A., Patel R., Pearce A.V., Peck A.I., Phillimore B.J.C.T., Phillips S., Plumb R.W., Porter K.M., Ramsey Y., Ranby S.A., Rice C.M., Ross M.T., Searle S.M., Sehra H.K., Sheridan E., Skuce C.D., Smith S., Smith M., Spraggon L., Squares S.L., Steward C.A., Sycamore N., Tamlyn-Hall G., Tester J., Theaker A.J., Thomas D.W., Thorpe A., Tracey A., Tromans A., Tubby B., Wall M., Wallis J.M., West A.P., White S.S., Whitehead S.L., Whittaker H., Wild A., Willey D.J., Wilmer T.E., Wood J.M., Wray P.W., Wyatt J.C., Young L., Younger R.M., Bentley D.R., Coulson A., Durbin R.M., Hubbard T., Sulston J.E., Dunham I., Rogers J., Beck S.
    Nature 425:805-811(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Pancreas.
  6. "Mammalian glycine N-methyltransferases. Comparative kinetic and structural properties of the enzymes from human, rat, rabbit and pig livers."
    Ogawa H., Gomi T., Fujioka M.
    Comp. Biochem. Physiol. 106B:601-611(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 31-295.
  7. "Glycine N-methyltransferases: a comparison of the crystal structures and kinetic properties of recombinant human, mouse and rat enzymes."
    Pakhomova S., Luka Z., Grohmann S., Wagner C., Newcomer M.E.
    Proteins 57:331-337(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.55 ANGSTROMS) OF 2-294, SUBUNIT, FUNCTION.
  8. "Destabilization of human glycine N-methyltransferase by H176N mutation."
    Luka Z., Pakhomova S., Luka Y., Newcomer M.E., Wagner C.
    Protein Sci. 16:1957-1964(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF 1-294, SUBUNIT, FUNCTION, CHARACTERIZATION OF VARIANT GNMT DEFICIENCY ASN-177.
  9. "Mutations in human glycine N-methyltransferase give insights into its role in methionine metabolism."
    Luka Z., Cerone R., Phillips J.A. III, Mudd S.H., Wagner C.
    Hum. Genet. 110:68-74(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: VARIANTS GNMT DEFICIENCY PRO-50 AND ASN-177.
  10. "Effect of naturally occurring mutations in human glycine N-methyltransferase on activity and conformation."
    Luka Z., Wagner C.
    Biochem. Biophys. Res. Commun. 312:1067-1072(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION OF VARIANTS GNMT DEFICIENCY PRO-50; SER-141 AND ASN-177.
  11. Cited for: VARIANT GNMT DEFICIENCY SER-141.

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: July 9, 2014
This is version 132 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

External Data

Dasty 3

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