2qvb

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(New page: 200px<br /><applet load="2qvb" size="350" color="white" frame="true" align="right" spinBox="true" caption="2qvb, resolution 1.190&Aring;" /> '''Crystal Structure o...)
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[[Image:2qvb.jpg|left|200px]]<br /><applet load="2qvb" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2qvb, resolution 1.190&Aring;" />
 
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'''Crystal Structure of Haloalkane Dehalogenase Rv2579 from Mycobacterium tuberculosis'''<br />
 
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==Overview==
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==Crystal Structure of Haloalkane Dehalogenase Rv2579 from Mycobacterium tuberculosis==
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Haloalkane dehalogenases are enzymes well known to be important in, bioremediation; the organisms from which they are produced are able to, clean up toxic organohalides from polluted environments. However, besides, being found in such contaminated environments, these enzymes have also, been found in root or tissue-colonizing bacterial species. The haloalkane, dehalogenase Rv2579 from Mycobacterium tuberculosis H37Rv has been cloned, expressed, purified and its crystal structure determined at high, resolution (1.2A). In addition, the crystal structure of the enzyme has, been determined in complex with the product from the reaction with, 1,3-dibromopropane, i.e. 1,3-propanediol and in complex with the classical, substrate of haloalkane dehalogenases, 1,2-dichloroethane. The enzyme is a, two-domain protein having a catalytic domain of an alpha/beta hydrolase, fold and a cap domain. The active site residues and the halide-stabilizing, residues have been identified as Asp109, Glu133, His273, Asn39 and Trp110., Its overall structure is similar to those of other known haloalkane, dehalogenases. Its mechanism of action involves an S(N)2 nucleophilic, displacement.
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<StructureSection load='2qvb' size='340' side='right'caption='[[2qvb]], [[Resolution|resolution]] 1.19&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2qvb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QVB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QVB 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]] 1.19&#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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=2qvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qvb OCA], [https://pdbe.org/2qvb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qvb RCSB], [https://www.ebi.ac.uk/pdbsum/2qvb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qvb ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DHAA_MYCTU DHAA_MYCTU] Catalyzes hydrolytic cleavage of carbon-halogen bonds in halogenated aliphatic compounds, leading to the formation of the corresponding primary alcohols, halide ions and protons (By similarity).[HAMAP-Rule:MF_01231]
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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/qv/2qvb_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=2qvb ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Haloalkane dehalogenases are enzymes well known to be important in bioremediation; the organisms from which they are produced are able to clean up toxic organohalides from polluted environments. However, besides being found in such contaminated environments, these enzymes have also been found in root or tissue-colonizing bacterial species. The haloalkane dehalogenase Rv2579 from Mycobacterium tuberculosis H37Rv has been cloned, expressed, purified and its crystal structure determined at high resolution (1.2A). In addition, the crystal structure of the enzyme has been determined in complex with the product from the reaction with 1,3-dibromopropane, i.e. 1,3-propanediol and in complex with the classical substrate of haloalkane dehalogenases, 1,2-dichloroethane. The enzyme is a two-domain protein having a catalytic domain of an alpha/beta hydrolase fold and a cap domain. The active site residues and the halide-stabilizing residues have been identified as Asp109, Glu133, His273, Asn39 and Trp110. Its overall structure is similar to those of other known haloalkane dehalogenases. Its mechanism of action involves an SN2 nucleophilic displacement.
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==About this Structure==
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X-ray crystal structure of Mycobacterium tuberculosis haloalkane dehalogenase Rv2579.,Mazumdar PA, Hulecki JC, Cherney MM, Garen CR, James MN Biochim Biophys Acta. 2008 Feb;1784(2):351-62. Epub 2007 Nov 13. PMID:18062934<ref>PMID:18062934</ref>
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2QVB 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 <scene name='pdbligand=CL:'>CL</scene> and <scene name='pdbligand=EDO:'>EDO</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Haloalkane_dehalogenase Haloalkane dehalogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.8.1.5 3.8.1.5] Known structural/functional Sites: <scene name='pdbsite=AC1:Cl+Binding+Site+For+Residue+A+2'>AC1</scene>, <scene name='pdbsite=AC2:Cl+Binding+Site+For+Residue+B+2'>AC2</scene>, <scene name='pdbsite=AC3:Edo+Binding+Site+For+Residue+A+1'>AC3</scene> and <scene name='pdbsite=AC4:Edo+Binding+Site+For+Residue+B+1'>AC4</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QVB OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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X-ray crystal structure of Mycobacterium tuberculosis haloalkane dehalogenase Rv2579., Mazumdar PA, Hulecki JC, Cherney MM, Garen CR, James MN, Biochim Biophys Acta. 2008 Feb;1784(2):351-62. Epub 2007 Nov 13. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=18062934 18062934]
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</div>
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[[Category: Haloalkane dehalogenase]]
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<div class="pdbe-citations 2qvb" style="background-color:#fffaf0;"></div>
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[[Category: Mycobacterium tuberculosis]]
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[[Category: Single protein]]
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[[Category: Cherney, M.M.]]
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[[Category: Garen, C.R.]]
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[[Category: Hulecki, J.]]
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[[Category: James, M.N.G.]]
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[[Category: Mazumdar, P.A.]]
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[[Category: TBSGC, TB.Structural.Genomics.Consortium.]]
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[[Category: CL]]
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[[Category: EDO]]
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[[Category: alpha-beta hydrolase protein]]
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[[Category: haloalkane dehalogenase]]
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[[Category: rv2579]]
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[[Category: tb structural genomics consortium]]
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[[Category: tbsgc]]
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[[Category: x-ray crystallography]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 13 08:21:07 2008''
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==See Also==
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*[[Dehalogenase 3D structures|Dehalogenase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Mycobacterium tuberculosis H37Rv]]
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[[Category: Cherney MM]]
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[[Category: Garen CR]]
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[[Category: Hulecki J]]
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[[Category: James MNG]]
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[[Category: Mazumdar PA]]

Current revision

Crystal Structure of Haloalkane Dehalogenase Rv2579 from Mycobacterium tuberculosis

PDB ID 2qvb

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