2hmk: Difference between revisions

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-{{Seed}}
-[[Image:2hmk.png|left|200px]]
-<!--
+==Crystal Structure of Naphthalene 1,2-Dioxygenase Bound to Phenanthrene==
-The line below this paragraph, containing "STRUCTURE_2hmk", creates the "Structure Box" on the page.
+<StructureSection load='2hmk' size='340' side='right'caption='[[2hmk]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2hmk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_sp. Pseudomonas sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HMK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HMK FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.65&#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=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=PEY:PHENANTHRENE'>PEY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_2hmk|  PDB=2hmk  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2hmk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hmk OCA], [https://pdbe.org/2hmk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hmk RCSB], [https://www.ebi.ac.uk/pdbsum/2hmk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hmk ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NDOB_PSEU8 NDOB_PSEU8] Component of the naphthalene dioxygenase (NDO) multicomponent enzyme system which catalyzes the incorporation of both atoms of molecular oxygen into naphthalene to form cis-naphthalene dihydrodiol.
+== 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/hm/2hmk_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=2hmk ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Rieske oxygenase (RO) systems are two- and three-component enzyme systems that catalyze the formation of cis-dihydrodiols from aromatic substrates. Degradation of pollutants in contaminated soil and generation of chiral synthons have been the major foci of RO research. Substrate specificity and product regio- and stereoselectivity have been shown to vary between individual ROs. While directed evolution methods for altering RO function have been successful in the past, rational engineering of these enzymes still poses a challenge due to the lack of structural understanding. Here we examine the structural changes induced by mutation of Phe-352 in naphthalene 1,2-dioxygenase from Pseudomonas sp. strain NCIB 9816-4 (NDO-O(9816-4)). Structures of the Phe-352-Val mutant in native form and in complex with phenanthrene and anthracene, along with those of wild-type NDO-O(9816-4) in complex with phenanthrene, anthracene, and 3-nitrotoluene, are presented. Phenanthrene was shown to bind in a different orientation in the Phe-352-Val mutant active site from that in the wild type, while anthracene was found to bind in similar positions in both enzymes. Two orientations of 3-nitrotoluene were observed, i.e., a productive and a nonproductive orientation. These orientations help explain why NDO-O(9816-4) forms different products from 3-nitrotoluene than those made from nitrobenzene dioxygenase. Comparison of these structures among themselves and with other known ROs bound to substrates reveals that the orientation of substrate binding at the active site is the primary determinant of product regio- and stereoselectivity.
-===Crystal Structure of Naphthalene 1,2-Dioxygenase Bound to Phenanthrene===
+Structural basis for regioselectivity and stereoselectivity of product formation by naphthalene 1,2-dioxygenase.,Ferraro DJ, Okerlund AL, Mowers JC, Ramaswamy S J Bacteriol. 2006 Oct;188(19):6986-94. PMID:16980501<ref>PMID:16980501</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2hmk" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_16980501}}, adds the Publication Abstract to the page
+*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 16980501 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16980501}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-HMK is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Pseudomonas_sp. Pseudomonas sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HMK OCA].
+[[Category: Pseudomonas sp]]
+[[Category: Ferraro DJ]]
-==Reference==
+[[Category: Mowers JC]]
-Structural basis for regioselectivity and stereoselectivity of product formation by naphthalene 1,2-dioxygenase., Ferraro DJ, Okerlund AL, Mowers JC, Ramaswamy S, J Bacteriol. 2006 Oct;188(19):6986-94. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16980501 16980501]
+[[Category: Okerlund AL]]
-[[Category: Naphthalene 1,2-dioxygenase]]
+[[Category: Ramaswamy S]]
-[[Category: Protein complex]]
-[[Category: Pseudomonas sp.]]
-[[Category: Ferraro, D J.]]
-[[Category: Mowers, J C.]]
-[[Category: Okerlund, A L.]]
-[[Category: Ramaswamy, S.]]
-[[Category: Oxioreductase]]
-[[Category: Protien]]
-[[Category: Rieske oxygenase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 04:02:54 2008''