1nbi

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[[Image:1nbi.jpg|left|200px]]
 
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{{Structure
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==Structure of R175K mutated glycine N-methyltransferase complexed with S-adenosylmethionine, R175K:SAM.==
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|PDB= 1nbi |SIZE=350|CAPTION= <scene name='initialview01'>1nbi</scene>, resolution 3.0&Aring;
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<StructureSection load='1nbi' size='340' side='right'caption='[[1nbi]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene>
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<table><tr><td colspan='2'>[[1nbi]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NBI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NBI FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycine_N-methyltransferase Glycine N-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.20 2.1.1.20] </span>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3&#8491;</td></tr>
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|GENE= GNMT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Rattus norvegicus])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr>
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|DOMAIN=
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1nbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nbi OCA], [https://pdbe.org/1nbi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nbi RCSB], [https://www.ebi.ac.uk/pdbsum/1nbi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nbi ProSAT]</span></td></tr>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1nbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nbi OCA], [http://www.ebi.ac.uk/pdbsum/1nbi PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1nbi RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/GNMT_RAT GNMT_RAT] 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.
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== Evolutionary Conservation ==
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'''Structure of R175K mutated glycine N-methyltransferase complexed with S-adenosylmethionine, R175K:SAM.'''
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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==Overview==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nb/1nbi_consurf.spt"</scriptWhenChecked>
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Methyltransfer reactions are some of the most important reactions in biological systems. Glycine N-methyltransferase (GNMT) catalyzes the S-adenosyl-l-methionine- (SAM-) dependent methylation of glycine to form sarcosine. Unlike most SAM-dependent methyltransferases, GNMT has a relatively high value and is weakly inhibited by the product S-adenosyl-l-homocysteine (SAH). The major role of GNMT is believed to be the regulation of the cellular SAM/SAH ratio, which is thought to play a key role in SAM-dependent methyltransfer reactions. Crystal structures of GNMT complexed with SAM and acetate (a potent competitive inhibitor of Gly) and the R175K mutated enzyme complexed with SAM were determined at 2.8 and 3.0 A resolutions, respectively. With these crystal structures and the previously determined structures of substrate-free enzyme, a catalytic mechanism has been proposed. Structural changes occur in the transitions from the substrate-free to the binary complex and from the binary to the ternary complex. In the ternary complex stage, an alpha-helix in the N-terminus undergoes a major conformational change. As a result, the bound SAM is firmly connected to protein and a "Gly pocket" is created near the bound SAM. The second substrate Gly binds to Arg175 and is brought into the Gly pocket. Five hydrogen bonds connect the Gly in the proximity of the bound SAM and orient the lone pair orbital on the amino nitrogen (N) of Gly toward the donor methyl group (C(E)) of SAM. Thermal motion of the enzyme leads to a collision of the N and C(E) so that a S(N)2 methyltransfer reaction occurs. The proposed mechanism is supported by mutagenesis studies.
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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==About this Structure==
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</jmolCheckbox>
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1NBI is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NBI OCA].
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1nbi ConSurf].
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<div style="clear:both"></div>
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==Reference==
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__TOC__
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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. 2003 Jul 22;42(28):8394-402. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12859184 12859184]
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</StructureSection>
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[[Category: Glycine N-methyltransferase]]
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[[Category: Large Structures]]
[[Category: Rattus norvegicus]]
[[Category: Rattus norvegicus]]
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[[Category: Single protein]]
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[[Category: Takata Y]]
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[[Category: Takata, Y.]]
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[[Category: Takusagawa F]]
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[[Category: Takusagawa, F.]]
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[[Category: catalytic mechanism]]
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[[Category: dynamical catalysis]]
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[[Category: glycine n-methyltransferase]]
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[[Category: methyltransferase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:28:01 2008''
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Current revision

Structure of R175K mutated glycine N-methyltransferase complexed with S-adenosylmethionine, R175K:SAM.

PDB ID 1nbi

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