2bmq: Difference between revisions

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-[[Image:2bmq.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_2bmq", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
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-{{STRUCTURE_2bmq|  PDB=2bmq  |  SCENE=  }}
-'''THE CRYSTAL STRUCTURE OF NITROBENZENE DIOXYGENASE IN COMPLEX WITH NITROBENZENE'''
+==The Crystal Structure of Nitrobenzene Dioxygenase in complex with nitrobenzene==
+<StructureSection load='2bmq' size='340' side='right'caption='[[2bmq]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2bmq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Comamonas_sp._JS765 Comamonas sp. JS765]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BMQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BMQ FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.55&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EOH:ETHANOL'>EOH</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=NBZ:NITROBENZENE'>NBZ</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2bmq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bmq OCA], [https://pdbe.org/2bmq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bmq RCSB], [https://www.ebi.ac.uk/pdbsum/2bmq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bmq ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q8RTL4_9BURK Q8RTL4_9BURK]
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bm/2bmq_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </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=2bmq ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Nitroaromatic compounds are used extensively in many industrial processes and have been released into the environment where they are considered environmental pollutants. Nitroaromatic compounds, in general, are resistant to oxidative attack due to the electron-withdrawing nature of the nitro groups and the stability of the benzene ring. However, the bacterium Comamonas sp. strain JS765 can grow with nitrobenzene as a sole source of carbon, nitrogen and energy. Biodegradation is initiated by the nitrobenzene dioxygenase (NBDO) system. We have determined the structure of NBDO, which has a hetero-hexameric structure similar to that of several other Rieske non-heme iron dioxygenases. The catalytic subunit contains a Rieske iron-sulfur center and an active-site mononuclear iron atom. The structures of complexes with substrates nitrobenzene and 3-nitrotoluene reveal the structural basis for its activity with nitroarenes. The substrate pocket contains an asparagine residue that forms a hydrogen bond to the nitro-group of the substrate, and orients the substrate in relation to the active-site mononuclear iron atom, positioning the molecule for oxidation at the nitro-substituted carbon.
-==Overview==
+Structural insight into the dioxygenation of nitroarene compounds: the crystal structure of nitrobenzene dioxygenase.,Friemann R, Ivkovic-Jensen MM, Lessner DJ, Yu CL, Gibson DT, Parales RE, Eklund H, Ramaswamy S J Mol Biol. 2005 May 20;348(5):1139-51. Epub 2005 Apr 7. PMID:15854650<ref>PMID:15854650</ref>
-Nitroaromatic compounds are used extensively in many industrial processes and have been released into the environment where they are considered environmental pollutants. Nitroaromatic compounds, in general, are resistant to oxidative attack due to the electron-withdrawing nature of the nitro groups and the stability of the benzene ring. However, the bacterium Comamonas sp. strain JS765 can grow with nitrobenzene as a sole source of carbon, nitrogen and energy. Biodegradation is initiated by the nitrobenzene dioxygenase (NBDO) system. We have determined the structure of NBDO, which has a hetero-hexameric structure similar to that of several other Rieske non-heme iron dioxygenases. The catalytic subunit contains a Rieske iron-sulfur center and an active-site mononuclear iron atom. The structures of complexes with substrates nitrobenzene and 3-nitrotoluene reveal the structural basis for its activity with nitroarenes. The substrate pocket contains an asparagine residue that forms a hydrogen bond to the nitro-group of the substrate, and orients the substrate in relation to the active-site mononuclear iron atom, positioning the molecule for oxidation at the nitro-substituted carbon.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-BMQ is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Comamonas_sp. Comamonas sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BMQ OCA].
+</div>
+<div class="pdbe-citations 2bmq" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Structural insight into the dioxygenation of nitroarene compounds: the crystal structure of nitrobenzene dioxygenase., Friemann R, Ivkovic-Jensen MM, Lessner DJ, Yu CL, Gibson DT, Parales RE, Eklund H, Ramaswamy S, J Mol Biol. 2005 May 20;348(5):1139-51. Epub 2005 Apr 7. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15854650 15854650]
+*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
-[[Category: Comamonas sp.]]
+== References ==
-[[Category: Protein complex]]
+<references/>
-[[Category: Eklund, H.]]
+__TOC__
-[[Category: Friemann, R.]]
+</StructureSection>
-[[Category: Gibson, D T.]]
+[[Category: Comamonas sp. JS765]]
-[[Category: Ivkovic-Jensen, M M.]]
+[[Category: Large Structures]]
-[[Category: Lessner, D J.]]
+[[Category: Eklund H]]
-[[Category: Parales, R E.]]
+[[Category: Friemann R]]
-[[Category: Ramaswamy, S.]]
+[[Category: Gibson DT]]
-[[Category: Yu, C.]]
+[[Category: Ivkovic-Jensen MM]]
-[[Category: Crystal structure]]
+[[Category: Lessner DJ]]
-[[Category: Metal-binding]]
+[[Category: Parales RE]]
-[[Category: Nad]]
+[[Category: Ramaswamy S]]
-[[Category: Nitroarene]]
+[[Category: Yu C]]
-[[Category: Nitrobenzene dioxygenase]]
-[[Category: Oxidoreductase]]
-[[Category: Rieske non-heme dioxygenase]]
-[[Category: Substrate specificity iron-sulfur]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 20:30:20 2008''