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1im8

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[[Image:1im8.gif|left|200px]]
 
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{{Structure
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==Crystal structure of YecO from Haemophilus influenzae (HI0319), a methyltransferase with a bound S-adenosylhomocysteine==
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|PDB= 1im8 |SIZE=350|CAPTION= <scene name='initialview01'>1im8</scene>, resolution 2.2&Aring;
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<StructureSection load='1im8' size='340' side='right'caption='[[1im8]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SAI:S-ADENOSYL-L-HOMOSELENOCYSTEINE'>SAI</scene>
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<table><tr><td colspan='2'>[[1im8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Haemophilus_influenzae_Rd_KW20 Haemophilus influenzae Rd KW20]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IM8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IM8 FirstGlance]. <br>
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|ACTIVITY=
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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]] 2.2&#8491;</td></tr>
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|GENE= HI0319 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 Haemophilus influenzae])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SAI:S-ADENOSYL-L-HOMOSELENOCYSTEINE'>SAI</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=1im8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1im8 OCA], [https://pdbe.org/1im8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1im8 RCSB], [https://www.ebi.ac.uk/pdbsum/1im8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1im8 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=1im8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1im8 OCA], [http://www.ebi.ac.uk/pdbsum/1im8 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1im8 RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/CMOA_HAEIN CMOA_HAEIN] Catalyzes the conversion of 5-methoxyuridine (mo5U) to uridine-5-oxyacetic acid (cmo5U) at position 34 in tRNA. May also participate in the methylation of uridine-5-oxyacetic acid (cmo5U) to uridine-5-oxyacetic acid methyl ester (mcmo5U) (By similarity).
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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/im/1im8_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=1im8 ConSurf].
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<div style="clear:both"></div>
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'''Crystal structure of YecO from Haemophilus influenzae (HI0319), a methyltransferase with a bound S-adenosylhomocysteine'''
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==See Also==
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*[[TRNA methyltransferase 3D structures|TRNA methyltransferase 3D structures]]
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__TOC__
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==Overview==
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</StructureSection>
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The crystal structure of YecO from Haemophilus influenzae (HI0319), a protein annotated in the sequence databases as hypothetical, and that has not been assigned a function, has been determined at 2.2-A resolution. The structure reveals a fold typical of S-adenosyl-L-methionine-dependent (AdoMet) methyltransferase enzymes. Moreover, a processed cofactor, S-adenosyl-L-homocysteine (AdoHcy), is bound to the enzyme, further confirming the biochemical function of HI0319 and its sequence family members. An active site arginine, shielded from bulk solvent, interacts with an anion, possibly a chloride ion, which in turn interacts with the sulfur atom of AdoHcy. The AdoHcy and nearby protein residues delineate a small solvent-excluded substrate binding cavity of 162 A(3) in volume. The environment surrounding the cavity indicates that the substrate molecule contains a hydrophobic moiety and an anionic group. Many of the residues that define the cavity are invariant in the HI0319 sequence family but are not conserved in other methyltransferases. Therefore, the substrate specificity of YecO enzymes is unique and differs from the substrate specificity of all other methyltransferases sequenced to date. Examination of the Enzyme Commission list of methyltransferases prompted a manual inspection of 10 possible substrates using computer graphics and suggested that the ortho-substituted benzoic acids fit best in the active site.
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[[Category: Haemophilus influenzae Rd KW20]]
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[[Category: Large Structures]]
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==About this Structure==
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[[Category: Bonander N]]
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1IM8 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IM8 OCA].
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[[Category: Eisenstein E]]
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[[Category: Herzberg O]]
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==Reference==
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[[Category: Howard A]]
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Crystal structure of YecO from Haemophilus influenzae (HI0319) reveals a methyltransferase fold and a bound S-adenosylhomocysteine., Lim K, Zhang H, Tempczyk A, Bonander N, Toedt J, Howard A, Eisenstein E, Herzberg O, Proteins. 2001 Dec 1;45(4):397-407. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11746687 11746687]
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[[Category: Lim K]]
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[[Category: Haemophilus influenzae]]
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[[Category: Tempczyk A]]
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[[Category: Single protein]]
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[[Category: Toedt J]]
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[[Category: Bonander, N.]]
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[[Category: Zhang H]]
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[[Category: Eisenstein, E.]]
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[[Category: Herzberg, O.]]
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[[Category: Howard, A.]]
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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: Toedt, J.]]
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[[Category: Zhang, H.]]
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[[Category: adenosylhomocysteine]]
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[[Category: hypothetical protein]]
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[[Category: methyltransferase]]
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[[Category: s2f]]
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[[Category: structural genomic]]
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[[Category: structure 2 function project]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:21:39 2008''
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Current revision

Crystal structure of YecO from Haemophilus influenzae (HI0319), a methyltransferase with a bound S-adenosylhomocysteine

PDB ID 1im8

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