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P13255

- GNMT_RAT

UniProt

P13255 - GNMT_RAT

Protein

Glycine N-methyltransferase

Gene

Gnmt

Organism
Rattus norvegicus (Rat)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 130 (01 Oct 2014)
      Sequence version 2 (23 Jan 2007)
      Previous versions | rss
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    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

    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

    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 – 101PhosphoserineBy similarity
    Modified residuei46 – 461N6-succinyllysineBy similarity
    Modified residuei191 – 1911N6-succinyllysineBy similarity
    Modified residuei196 – 1961N6-succinyllysineBy similarity
    Modified residuei201 – 2011N6-succinyllysineBy 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.1 Publication

    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.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP13255.

    Family & Domainsi

    Region

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

    Sequence similaritiesi

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

    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: October 1, 2014
    This is version 130 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