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| - | [[Image:1nxj.gif|left|200px]] | |
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| - | {{Structure
| + | ==Structure of Rv3853 from Mycobacterium tuberculosis== |
| - | |PDB= 1nxj |SIZE=350|CAPTION= <scene name='initialview01'>1nxj</scene>, resolution 1.90Å
| + | <StructureSection load='1nxj' size='340' side='right'caption='[[1nxj]], [[Resolution|resolution]] 1.90Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=GLV:GLYOXYLIC+ACID'>GLV</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene> | + | <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> |
| - | |ACTIVITY=
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9Å</td></tr> |
| - | |GENE= MENG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 Mycobacterium tuberculosis])
| + | <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> |
| - | |DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PRK09372 PRK09372]</span>
| + | <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> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1nxj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nxj OCA], [http://www.ebi.ac.uk/pdbsum/1nxj PDBsum], [http://www.fli-leibniz.de/cgi-bin/ImgLib.pl?CODE=1kfv JenaLib], [http://www.rcsb.org/pdb/explore.do?structureId=1nxj RCSB]</span>
| + | </table> |
| - | }}
| + | == Function == |
| - | | + | [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). |
| - | '''Structure of Rv3853 from Mycobacterium tuberculosis'''
| + | == Evolutionary Conservation == |
| - | | + | [[Image:Consurf_key_small.gif|200px|right]] |
| - | | + | Check<jmol> |
| - | ==Overview== | + | <jmolCheckbox> |
| - | 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.
| + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nx/1nxj_consurf.spt"</scriptWhenChecked> |
| - | | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| - | ==About this Structure== | + | <text>to colour the structure by Evolutionary Conservation</text> |
| - | 1NXJ is a [[Single protein]] structure of sequence from [http://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].
| + | </jmolCheckbox> |
| - | | + | </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]. |
| - | ==Reference==
| + | <div style="clear:both"></div> |
| - | 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://www.ncbi.nlm.nih.gov/pubmed/12837779 12837779]
| + | __TOC__ |
| | + | </StructureSection> |
| | + | [[Category: Large Structures]] |
| | [[Category: Mycobacterium tuberculosis]] | | [[Category: Mycobacterium tuberculosis]] |
| - | [[Category: Single protein]]
| + | [[Category: Arcus VL]] |
| - | [[Category: Arcus, V L.]] | + | [[Category: Baker EN]] |
| - | [[Category: Baker, E N.]] | + | [[Category: Johnston JM]] |
| - | [[Category: Johnston, J M.]] | + | |
| - | [[Category: TBSGC, TB Structural Genomics Consortium.]]
| + | |
| - | [[Category: beta/beta/alpha domain]]
| + | |
| - | [[Category: protein structure initiative]]
| + | |
| - | [[Category: psi]]
| + | |
| - | [[Category: structural genomic]]
| + | |
| - | [[Category: tb structural genomics consortium]]
| + | |
| - | [[Category: tbsgc]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 26 05:59:24 2008''
| + | |
