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P13255

- GNMT_RAT

UniProt

P13255 - GNMT_RAT

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Protein

Glycine N-methyltransferase

Gene
Gnmt
Organism
Rattus norvegicus (Rat)
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.

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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei22 – 221S-adenosyl-L-methionine
Binding sitei31 – 311S-adenosyl-L-methionine
Binding sitei34 – 341Substrate
Binding sitei41 – 411S-adenosyl-L-methionine
Binding sitei65 – 651S-adenosyl-L-methionine; via carbonyl oxygen
Binding sitei86 – 861S-adenosyl-L-methionine
Binding sitei137 – 1371S-adenosyl-L-methionine; via carbonyl oxygen
Binding sitei139 – 1391Substrate
Binding sitei176 – 1761Substrate
Binding sitei221 – 2211Substrate

GO - Molecular functioni

  1. folic acid binding Source: RGD
  2. glycine binding Source: UniProtKB
  3. glycine N-methyltransferase activity Source: UniProtKB
  4. S-adenosylmethionine-dependent methyltransferase activity Source: RGD

GO - Biological processi

  1. folic acid metabolic process Source: RGD
  2. glycine metabolic process Source: RGD
  3. protein homotetramerization Source: UniProtKB
  4. protein tetramerization Source: RGD
  5. S-adenosylhomocysteine metabolic process Source: RGD
  6. S-adenosylmethionine metabolic process Source: UniProtKB
  7. sarcosine metabolic process Source: RGD
Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Ligandi

Folate-binding, S-adenosyl-L-methionine

Enzyme and pathway databases

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
ProteomesiUP000002494: Chromosome 9

Organism-specific databases

RGDi2719. Gnmt.

Subcellular locationi

GO - Cellular componenti

  1. cytosol Source: RGD
  2. nucleus Source: RGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi34 – 341Y → F: Reduces affinity for glycine. 1 Publication
Mutagenesisi176 – 1761R → K: Strongly reduced affinity for glycine. 1 Publication
Mutagenesisi221 – 2211Y → F: Reduces affinity for glycine. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 293292Glycine N-methyltransferasePRO_0000087528Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylvaline1 Publication
Modified residuei10 – 101Phosphoserine By similarity
Modified residuei46 – 461N6-succinyllysine By similarity
Modified residuei191 – 1911N6-succinyllysine By similarity
Modified residuei196 – 1961N6-succinyllysine By similarity
Modified residuei201 – 2011N6-succinyllysine By similarity

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

PaxDbiP13255.
PRIDEiP13255.

PTM databases

PhosphoSiteiP13255.

Expressioni

Tissue specificityi

Abundant in liver.

Gene expression databases

GenevestigatoriP13255.

Interactioni

Subunit structurei

Homotetramer.

Protein-protein interaction databases

MINTiMINT-4567246.
STRINGi10116.ENSRNOP00000022307.

Structurei

Secondary structure

1
293
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi5 – 95
Beta strandi11 – 133
Turni21 – 244
Helixi26 – 3510
Beta strandi39 – 413
Helixi43 – 5513
Beta strandi60 – 634
Helixi70 – 778
Beta strandi81 – 877
Helixi89 – 10113
Turni102 – 1043
Helixi106 – 1094
Beta strandi112 – 1154
Helixi118 – 1203
Helixi121 – 1244
Beta strandi131 – 1366
Turni137 – 1393
Helixi141 – 1433
Beta strandi147 – 1515
Helixi152 – 16312
Beta strandi165 – 17612
Helixi178 – 1847
Beta strandi193 – 1953
Beta strandi202 – 2109
Beta strandi213 – 22513
Beta strandi229 – 2324
Beta strandi235 – 2439
Helixi248 – 25710
Turni258 – 2614
Beta strandi263 – 2697
Beta strandi283 – 2919

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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. Positions 2-293.

Miscellaneous databases

EvolutionaryTraceiP13255.

Family & Domainsi

Region

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

Sequence similaritiesi

Phylogenomic databases

eggNOGiNOG78825.
GeneTreeiENSGT00390000006845.
HOGENOMiHOG000276537.
HOVERGENiHBG051748.
InParanoidiP13255.
KOiK00552.
OMAiLIIDHRN.
OrthoDBiEOG76QFHR.
PhylomeDBiP13255.
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.

P13255-1 [UniParc]FASTAAdd to Basket

« Hide

MVDSVYRTRS LGVAAEGIPD QYADGEAARV WQLYIGDTRS RTAEYKAWLL    50
GLLRQHGCHR VLDVACGTGV DSIMLVEEGF SVTSVDASDK MLKYALKERW 100
NRRKEPAFDK WVIEEANWLT LDKDVPAGDG FDAVICLGNS FAHLPDSKGD 150
QSEHRLALKN IASMVRPGGL LVIDHRNYDY ILSTGCAPPG KNIYYKSDLT 200
KDITTSVLTV NNKAHMVTLD YTVQVPGAGR DGAPGFSKFR LSYYPHCLAS 250
FTELVQEAFG GRCQHSVLGD FKPYRPGQAY VPCYFIHVLK KTG 293
Length:293
Mass (Da):32,549
Last modified:January 23, 2007 - v2
Checksum:i4E98C7512F0228A5
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
Links Updated
X06150 mRNA. Translation: CAA29508.1 .
X07833 Genomic DNA. Translation: CAA30686.1 .
PIRi S00112.
RefSeqi NP_058780.1. NM_017084.1.
UniGenei Rn.11142.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1BHJ X-ray 2.50 A/B 2-293 [» ]
1D2C X-ray 2.50 A/B 2-293 [» ]
1D2G X-ray 2.50 A/B 2-293 [» ]
1D2H X-ray 3.00 A/B/C/D 2-293 [» ]
1KIA X-ray 2.80 A/B/C/D 2-293 [» ]
1NBH X-ray 2.80 A/B/C/D 2-293 [» ]
1NBI X-ray 3.00 A/B/C/D 2-293 [» ]
1XVA X-ray 2.20 A/B 2-293 [» ]
2IDJ X-ray 2.35 A/B/C/D 2-293 [» ]
2IDK X-ray 2.55 A/B/C/D 2-293 [» ]
3THR X-ray 2.00 A/B/C/D 2-293 [» ]
3THS X-ray 2.50 A/B/C/D 2-293 [» ]
DisProti DP00031.
ProteinModelPortali P13255.
SMRi P13255. Positions 2-293.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

MINTi MINT-4567246.
STRINGi 10116.ENSRNOP00000022307.

PTM databases

PhosphoSitei P13255.

Proteomic databases

PaxDbi P13255.
PRIDEi P13255.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENSRNOT00000022307 ; ENSRNOP00000022307 ; ENSRNOG00000016349 .
GeneIDi 25134.
KEGGi rno:25134.
UCSCi RGD:2719. rat.

Organism-specific databases

CTDi 27232.
RGDi 2719. Gnmt.

Phylogenomic databases

eggNOGi NOG78825.
GeneTreei ENSGT00390000006845.
HOGENOMi HOG000276537.
HOVERGENi HBG051748.
InParanoidi P13255.
KOi K00552.
OMAi LIIDHRN.
OrthoDBi EOG76QFHR.
PhylomeDBi P13255.
TreeFami TF324814.

Enzyme and pathway databases

SABIO-RK P13255.

Miscellaneous databases

EvolutionaryTracei P13255.
NextBioi 605549.
PROi P13255.

Gene expression databases

Genevestigatori P13255.

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

  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. 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.

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: July 9, 2014
This is version 129 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

External Data

Dasty 3

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