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1mxi

From Proteopedia

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[[Image:1mxi.gif|left|200px]]<br /><applet load="1mxi" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1mxi, resolution 1.7&Aring;" />
 
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'''Structure of YibK from Haemophilus influenzae (HI0766): a Methyltransferase with a Cofactor Bound at a Site Formed by a Knot'''<br />
 
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==Overview==
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==Structure of YibK from Haemophilus influenzae (HI0766): a Methyltransferase with a Cofactor Bound at a Site Formed by a Knot==
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The crystal structures of YibK from Haemophilus influenzae (HI0766) have been determined with and without bound cofactor product S-adenosylhomocysteine (AdoHcy) at 1.7 and 2.0 A resolution, respectively. The molecule adopts an alpha/beta fold, with a topology that differs from that of the classical methyltransferases. Most notably, HI0766 contains a striking knot that forms the binding crevice for the cofactor. The knot formation is correlated with an alternative arrangement of the secondary structure units compared with the classical methyltransferases. Two loop regions undergo conformational changes upon AdoHcy binding. In contrast to the extended conformation of the cofactor seen in the classical methyltransferase structures, AdoHcy binds to HI0766 in a bent conformation. HI0766 and its close sequence relatives are all shorter versions of the more remotely related rRNA/tRNA methyltransferases of the spoU sequence family. We propose that the spoU sequence family contains the same core domain for cofactor binding as HI0766 but has an additional domain for substrate binding. The substrate-binding domain is absent in HI0766 sequence family and may be provided by another Haemophilus influenzae partner protein, which is yet to be identified.
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<StructureSection load='1mxi' size='340' side='right'caption='[[1mxi]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1mxi]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MXI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MXI 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]] 1.7&#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=IOD:IODIDE+ION'>IOD</scene>, <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=1mxi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mxi OCA], [https://pdbe.org/1mxi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mxi RCSB], [https://www.ebi.ac.uk/pdbsum/1mxi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mxi ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/TRML_HAEIN TRML_HAEIN] Methylates the ribose at the nucleotide 34 wobble position in the two leucyl isoacceptors tRNA(Leu)(CmAA) and tRNA(Leu)(cmnm5UmAA). Catalyzes the methyl transfer from S-adenosyl-L-methionine to the 2'-OH of the wobble nucleotide.[HAMAP-Rule:MF_01885]
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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/mx/1mxi_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=1mxi 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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1MXI is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae] with <scene name='pdbligand=IOD:'>IOD</scene> and <scene name='pdbligand=SAH:'>SAH</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MXI OCA].
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*[[TRNA methyltransferase 3D structures|TRNA methyltransferase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Structure of the YibK methyltransferase from Haemophilus influenzae (HI0766): a cofactor bound at a site formed by a knot., Lim K, Zhang H, Tempczyk A, Krajewski W, Bonander N, Toedt J, Howard A, Eisenstein E, Herzberg O, Proteins. 2003 Apr 1;51(1):56-67. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12596263 12596263]
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[[Category: Haemophilus influenzae]]
[[Category: Haemophilus influenzae]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Bonander, N.]]
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[[Category: Bonander N]]
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[[Category: Eisenstein, E.]]
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[[Category: Eisenstein E]]
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[[Category: Herzberg, O.]]
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[[Category: Herzberg O]]
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[[Category: Howard, A.]]
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[[Category: Howard A]]
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[[Category: Lim, K.]]
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[[Category: Lim K]]
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[[Category: S2F, Structure 2.Function Project.]]
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[[Category: Tempczyk A]]
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[[Category: Tempczyk, A.]]
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[[Category: Toedt J]]
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[[Category: Toedt, J.]]
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[[Category: Zhang H]]
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[[Category: Zhang, H.]]
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[[Category: IOD]]
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[[Category: SAH]]
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[[Category: methyltransferase]]
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[[Category: s-adenosylhomocysteine]]
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[[Category: s2f]]
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[[Category: spou family]]
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[[Category: structural genomics]]
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[[Category: structure 2 function project]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:00:07 2008''
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Current revision

Structure of YibK from Haemophilus influenzae (HI0766): a Methyltransferase with a Cofactor Bound at a Site Formed by a Knot

PDB ID 1mxi

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