1nxj

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(New page: 200px<br /><applet load="1nxj" size="450" color="white" frame="true" align="right" spinBox="true" caption="1nxj, resolution 1.90&Aring;" /> '''Structure of Rv3853 ...)
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[[Image:1nxj.gif|left|200px]]<br /><applet load="1nxj" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1nxj, resolution 1.90&Aring;" />
 
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'''Structure of Rv3853 from Mycobacterium tuberculosis'''<br />
 
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==Overview==
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==Structure of Rv3853 from Mycobacterium tuberculosis==
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Bioinformatic analyses of whole genome sequences highlight the problem of, identifying the biochemical and cellular functions of many gene products, that are at present uncharacterized. The open reading frame Rv3853 from, Mycobacterium tuberculosis has been annotated as menG and assumed to, encode an S-adenosylmethionine (SAM)-dependent methyltransferase that, catalyzes the final step in menaquinone biosynthesis. The Rv3853 gene, product has been expressed, refolded, purified, and crystallized in the, context of a structural genomics program. Its crystal structure has been, determined by isomorphous replacement and refined at 1.9 A resolution to, an R factor of 19.0% and R(free) of 22.0%. The structure strongly suggests, that this protein is not a SAM-dependent methyltransferase and that the, gene has been misannotated in this and other genomes that contain, homologs. The protein forms a tightly associated, disk-like trimer. The, monomer fold is unlike that of any known SAM-dependent methyltransferase, most closely resembling the phosphohistidine domains of several, phosphotransfer systems. Attempts to bind cofactor and substrate molecules, have been unsuccessful, but two adventitiously bound small-molecule, ligands, modeled as tartrate and glyoxalate, are present on each monomer., These may point to biologically relevant binding sites but do not suggest, a function. In silico screening indicates a range of ligands that could, occupy these and other sites. The nature of these ligands, coupled with, the location of binding sites on the trimer, suggests that proteins of the, Rv3853 family, which are distributed throughout microbial and plant, species, may be part of a larger assembly binding to nucleic acids or, proteins.
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<StructureSection load='1nxj' size='340' side='right'caption='[[1nxj]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1nxj]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NXJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NXJ FirstGlance]. <br>
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1NXJ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis] with GLV and TLA as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1NXJ OCA].
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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]] 1.9&#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=GLV:GLYOXYLIC+ACID'>GLV</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
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==Reference==
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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=1nxj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nxj OCA], [https://pdbe.org/1nxj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nxj RCSB], [https://www.ebi.ac.uk/pdbsum/1nxj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nxj ProSAT]</span></td></tr>
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Crystal structure of a putative methyltransferase from Mycobacterium tuberculosis: misannotation of a genome clarified by protein structural analysis., Johnston JM, Arcus VL, Morton CJ, Parker MW, Baker EN, J Bacteriol. 2003 Jul;185(14):4057-65. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12837779 12837779]
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RRAAH_MYCTU RRAAH_MYCTU] Catalyzes the aldol cleavage of 4-hydroxy-4-methyl-2-oxoglutarate (HMG) into 2 molecules of pyruvate. Also contains a secondary oxaloacetate (OAA) decarboxylase activity due to the common pyruvate enolate transition state formed following C-C bond cleavage in the retro-aldol and decarboxylation reactions (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/nx/1nxj_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=1nxj ConSurf].
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<div style="clear:both"></div>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Mycobacterium tuberculosis]]
[[Category: Mycobacterium tuberculosis]]
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[[Category: Single protein]]
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[[Category: Arcus VL]]
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[[Category: Arcus, V.L.]]
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[[Category: Baker EN]]
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[[Category: Baker, E.N.]]
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[[Category: Johnston JM]]
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[[Category: Johnston, J.M.]]
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[[Category: TBSGC, TB.Structural.Genomics.Consortium.]]
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[[Category: GLV]]
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[[Category: TLA]]
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[[Category: beta/beta/alpha domain]]
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[[Category: protein structure initiative]]
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[[Category: psi]]
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[[Category: structural genomics]]
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[[Category: tb structural genomics consortium]]
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[[Category: tbsgc]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 22:38:40 2007''
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Current revision

Structure of Rv3853 from Mycobacterium tuberculosis

PDB ID 1nxj

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