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P13255 (GNMT_RAT) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 129. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Glycine N-methyltransferase

EC=2.1.1.20
Alternative name(s):
Folate-binding protein
Gene names
Name:Gnmt
OrganismRattus norvegicus (Rat) [Reference proteome]
Taxonomic identifier10116 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus

Protein attributes

Sequence length293 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

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. Ref.6

Subunit structure

Homotetramer.

Subcellular location

Cytoplasm.

Tissue specificity

Abundant in liver.

Sequence similarities

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.1
Chain2 – 293292Glycine N-methyltransferase
PRO_0000087528

Regions

Region117 – 1182S-adenosyl-L-methionine binding

Sites

Binding site221S-adenosyl-L-methionine
Binding site311S-adenosyl-L-methionine
Binding site341Substrate
Binding site411S-adenosyl-L-methionine
Binding site651S-adenosyl-L-methionine; via carbonyl oxygen
Binding site861S-adenosyl-L-methionine
Binding site1371S-adenosyl-L-methionine; via carbonyl oxygen
Binding site1391Substrate
Binding site1761Substrate
Binding site2211Substrate

Amino acid modifications

Modified residue21N-acetylvaline Ref.1
Modified residue101Phosphoserine By similarity
Modified residue461N6-succinyllysine By similarity
Modified residue1911N6-succinyllysine By similarity
Modified residue1961N6-succinyllysine By similarity
Modified residue2011N6-succinyllysine By similarity

Experimental info

Mutagenesis341Y → F: Reduces affinity for glycine. Ref.5
Mutagenesis1761R → K: Strongly reduced affinity for glycine. Ref.5
Mutagenesis2211Y → F: Reduces affinity for glycine. Ref.5

Secondary structure

.......................................................... 293
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P13255 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: 4E98C7512F0228A5

FASTA29332,549
        10         20         30         40         50         60 
MVDSVYRTRS LGVAAEGIPD QYADGEAARV WQLYIGDTRS RTAEYKAWLL GLLRQHGCHR 

        70         80         90        100        110        120 
VLDVACGTGV DSIMLVEEGF SVTSVDASDK MLKYALKERW NRRKEPAFDK WVIEEANWLT 

       130        140        150        160        170        180 
LDKDVPAGDG FDAVICLGNS FAHLPDSKGD QSEHRLALKN IASMVRPGGL LVIDHRNYDY 

       190        200        210        220        230        240 
ILSTGCAPPG KNIYYKSDLT KDITTSVLTV NNKAHMVTLD YTVQVPGAGR DGAPGFSKFR 

       250        260        270        280        290 
LSYYPHCLAS FTELVQEAFG GRCQHSVLGD FKPYRPGQAY VPCYFIHVLK KTG 

« Hide

References

[1]"Rat glycine methyltransferase. Complete amino acid sequence deduced from a cDNA clone and characterization of the genomic DNA."
Ogawa H., Konishi K., Takata Y., Nakashima H., Fujioka M.
Eur. J. Biochem. 168:141-151(1987) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA], PROTEIN SEQUENCE OF 2-7, CLEAVAGE OF INITIATOR METHIONINE, ACETYLATION AT VAL-2.
Strain: Sprague-Dawley.
[2]"Crystal structure of glycine N-methyltransferase from rat liver."
Fu Z., Hu Y., Konishi K., Takata Y., Ogawa H., Gomi T., Fujioka M., Takusagawa F.
Biochemistry 35:11985-11993(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
Tissue: Liver.
[3]"Crystal structure of apo-glycine N-methyltransferase (GNMT)."
Pattanayek R., Newcomer M.E., Wagner C.
Protein Sci. 7:1326-1331(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
[4]"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."
Huang Y., Komoto J., Konishi K., Takata Y., Ogawa H., Gomi T., Fujioka M., Takusagawa F.
J. Mol. Biol. 298:149-162(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
[5]"Catalytic mechanism of glycine N-methyltransferase."
Takata Y., Huang Y., Komoto J., Yamada T., Konishi K., Ogawa H., Gomi T., Fujioka M., Takusagawa F.
Biochemistry 42:8394-8402(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 2-292 IN COMPLEXES WITH S-ADENOSYL-L-METHIONINE AND ACETATE, MUTAGENESIS OF TYR-34; ARG-176 AND TYR-221.
[6]"5-methyltetrahydrofolate is bound in intersubunit areas of rat liver folate-binding protein glycine N-methyltransferase."
Luka Z., Pakhomova S., Loukachevitch L.V., Egli M., Newcomer M.E., Wagner C.
J. Biol. Chem. 282:4069-4075(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS) OF 2-292 IN COMPLEX WITH 5-METHYLTETRAHYDROFOLATE, ENZYME REGULATION.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X06150 mRNA. Translation: CAA29508.1.
X07833 Genomic DNA. Translation: CAA30686.1.
PIRS00112.
RefSeqNP_058780.1. NM_017084.1.
UniGeneRn.11142.

3D structure databases

PDBe
RCSB-PDB
PDBj
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[»]
DisProtDP00031.
ProteinModelPortalP13255.
SMRP13255. Positions 2-293.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

MINTMINT-4567246.
STRING10116.ENSRNOP00000022307.

PTM databases

PhosphoSiteP13255.

Proteomic databases

PaxDbP13255.
PRIDEP13255.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSRNOT00000022307; ENSRNOP00000022307; ENSRNOG00000016349.
GeneID25134.
KEGGrno:25134.
UCSCRGD:2719. rat.

Organism-specific databases

CTD27232.
RGD2719. Gnmt.

Phylogenomic databases

eggNOGNOG78825.
GeneTreeENSGT00390000006845.
HOGENOMHOG000276537.
HOVERGENHBG051748.
InParanoidP13255.
KOK00552.
OMALIIDHRN.
OrthoDBEOG76QFHR.
PhylomeDBP13255.
TreeFamTF324814.

Enzyme and pathway databases

SABIO-RKP13255.

Gene expression databases

GenevestigatorP13255.

Family and domain databases

Gene3D3.40.50.150. 1 hit.
InterProIPR014369. Gly/Sar_N_MeTrfase.
IPR029063. SAM-dependent_MTases-like.
[Graphical view]
PANTHERPTHR16458. PTHR16458. 1 hit.
PIRSFPIRSF000385. Gly_N-mtase. 1 hit.
SUPFAMSSF53335. SSF53335. 1 hit.
PROSITEPS51600. SAM_GNMT. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP13255.
NextBio605549.
PROP13255.

Entry information

Entry nameGNMT_RAT
AccessionPrimary (citable) accession number: P13255
Entry history
Integrated into UniProtKB/Swiss-Prot: January 1, 1990
Last sequence update: January 23, 2007
Last modified: July 9, 2014
This is version 129 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references