1p9p

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[[Image:1p9p.gif|left|200px]]<br /><applet load="1p9p" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1p9p, resolution 2.5&Aring;" />
 
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'''The Crystal Structure of a M1G37 tRNA Methyltransferase, TrmD'''<br />
 
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==Overview==
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==The Crystal Structure of a M1G37 tRNA Methyltransferase, TrmD==
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The crystal structure of Escherichia coli tRNA (guanosine-1) methyltransferase (TrmD) complexed with S-adenosyl homocysteine (AdoHcy) has been determined at 2.5A resolution. TrmD, which methylates G37 of tRNAs containing the sequence G36pG37, is a homo-dimer. Each monomer consists of a C-terminal domain connected by a flexible linker to an N-terminal AdoMet-binding domain. The two bound AdoHcy moieties are buried at the bottom of deep clefts. The dimer structure appears integral to the formation of the catalytic center of the enzyme and this arrangement strongly suggests that the anticodon loop of tRNA fits into one of these clefts for methyl transfer to occur. In addition, adjacent hydrophobic sites in the cleft delineate a defined pocket, which may accommodate the GpG sequence during catalysis. The dimer contains two deep trefoil peptide knots and a peptide loop extending from each knot embraces the AdoHcy adenine ring. Mutational analyses demonstrate that the knot is important for AdoMet binding and catalytic activity, and that the C-terminal domain is not only required for tRNA binding but plays a functional role in catalytic activity.
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<StructureSection load='1p9p' size='340' side='right'caption='[[1p9p]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1p9p]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P9P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1P9P FirstGlance]. <br>
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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]] 2.5&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
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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=1p9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p9p OCA], [https://pdbe.org/1p9p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1p9p RCSB], [https://www.ebi.ac.uk/pdbsum/1p9p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1p9p ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/TRMD_ECOLI TRMD_ECOLI] Specifically methylates guanosine-37 in various tRNAs.<ref>PMID:14583191</ref>
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== Evolutionary Conservation ==
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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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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/p9/1p9p_consurf.spt"</scriptWhenChecked>
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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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</jmolCheckbox>
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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=1p9p ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1P9P is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli,_escherichia_coli_o6,_escherichia_coli_o157:h7,_and_shigella_flexneri Escherichia coli, escherichia coli o6, escherichia coli o157:h7, and shigella flexneri] with <scene name='pdbligand=SAH:'>SAH</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/tRNA_(guanine-N(1)-)-methyltransferase tRNA (guanine-N(1)-)-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.31 2.1.1.31] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P9P OCA].
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*[[TRNA methyltransferase 3D structures|TRNA methyltransferase 3D structures]]
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== References ==
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==Reference==
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<references/>
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Insights into catalysis by a knotted TrmD tRNA methyltransferase., Elkins PA, Watts JM, Zalacain M, van Thiel A, Vitazka PR, Redlak M, Andraos-Selim C, Rastinejad F, Holmes WM, J Mol Biol. 2003 Nov 7;333(5):931-49. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=14583191 14583191]
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__TOC__
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[[Category: Escherichia coli, escherichia coli o6, escherichia coli o157:h7, and shigella flexneri]]
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</StructureSection>
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[[Category: Single protein]]
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[[Category: Escherichia coli K-12]]
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[[Category: tRNA (guanine-N(1)-)-methyltransferase]]
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[[Category: Large Structures]]
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[[Category: Andraos-Selim, C.]]
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[[Category: Andraos-Selim C]]
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[[Category: Elkins, P A.]]
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[[Category: Elkins PA]]
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[[Category: Holmes, W M.]]
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[[Category: Holmes WM]]
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[[Category: Rastinejad, F.]]
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[[Category: Rastinejad F]]
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[[Category: Redlak, M.]]
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[[Category: Redlak M]]
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[[Category: Thiel, A Van.]]
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[[Category: Van Thiel A]]
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[[Category: Vitaszka, P R.]]
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[[Category: Vitaszka PR]]
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[[Category: Watts, J M.]]
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[[Category: Watts JM]]
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[[Category: Zalacain, M.]]
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[[Category: Zalacain M]]
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[[Category: SAH]]
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[[Category: adomet]]
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[[Category: knot]]
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[[Category: methyltransferase]]
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[[Category: s-adenosylmethionine]]
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[[Category: spou]]
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[[Category: spout]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:26:40 2008''
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Current revision

The Crystal Structure of a M1G37 tRNA Methyltransferase, TrmD

PDB ID 1p9p

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