3dr9: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
 ==Increased Distal Histidine Conformational Flexibility in the Deoxy Form of Dehaloperoxidase from Amphitrite ornata==
-<StructureSection load='3dr9' size='340' side='right' caption='[[3dr9]], [[Resolution|resolution]] 1.26&Aring;' scene=''>
+<StructureSection load='3dr9' size='340' side='right'caption='[[3dr9]], [[Resolution|resolution]] 1.26&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3dr9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Amphitrite_ornata Amphitrite ornata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DR9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DR9 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3dr9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Amphitrite_ornata Amphitrite ornata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DR9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DR9 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.26&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dhpA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=129555 Amphitrite ornata])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3dr9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dr9 OCA], [http://pdbe.org/3dr9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dr9 RCSB], [http://www.ebi.ac.uk/pdbsum/3dr9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3dr9 ProSAT]</span></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=3dr9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dr9 OCA], [https://pdbe.org/3dr9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dr9 RCSB], [https://www.ebi.ac.uk/pdbsum/3dr9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dr9 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9NAV8_9ANNE Q9NAV8_9ANNE]
 == 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/dr/3dr9_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dr/3dr9_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 18: / Line 20: @@
 </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=3dr9 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The enzyme dehaloperoxidase (DHP) from the terebellid polychaete Amphitrite ornata is a heme protein which has a globin fold but can function as both a hemoglobin and a peroxidase. As a peroxidase, DHP is capable of converting 2,4,6-trihalophenols to the corresponding 2,6-dihaloquinones in the presence of hydrogen peroxide. As a hemoglobin, DHP cycles between the oxy and deoxy states as it reversibly binds oxygen for storage. Here, it is reported that the distal histidine, His55, exhibits conformational flexibility in the deoxy form and is consequently observed in two solvent-exposed conformations more than 9.5 A away from the heme. These conformations are analogous to the open conformation of sperm whale myoglobin. The heme iron in deoxy ferrous DHP is five-coordinate and has an out-of-plane displacement of 0.25 A from the heme plane. The observation of five-coordinate heme iron with His55 in a remote solvent-exposed conformation is consistent with the hypothesis that His55 interacts with heme iron ligands through hydrogen bonding in the closed conformation. Since His55 is also displaced by the binding of 4-iodophenol in an internal pocket, these results provide new insight into the correlation between heme iron ligation, molecular binding in the distal pocket and the conformation of the distal histidine in DHP.
-Distal histidine conformational flexibility in dehaloperoxidase from Amphitrite ornata.,Chen Z, de Serrano V, Betts L, Franzen S Acta Crystallogr D Biol Crystallogr. 2009 Jan;65(Pt 1):34-40. Epub 2008, Dec 18. PMID:19153464<ref>PMID:19153464</ref>
+==See Also==
+*[[Dehaloperoxidase 3D structures|Dehaloperoxidase 3D structures]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3dr9" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
 [[Category: Amphitrite ornata]]
-[[Category: Betts, L]]
+[[Category: Large Structures]]
-[[Category: Chen, X]]
+[[Category: Betts L]]
-[[Category: Franzen, S]]
+[[Category: Chen X]]
-[[Category: Serrano, V S.de]]
+[[Category: Franzen S]]
-[[Category: Deoxy form of dehaloperoxidase]]
+[[Category: De Serrano VS]]
-[[Category: Dhp]]
-[[Category: Globin]]
-[[Category: Globin-like]]
-[[Category: Heme]]
-[[Category: Heme peroxidase]]
-[[Category: Heme protein]]
-[[Category: Oxidoreductase]]
-[[Category: Oxygen transport]]
-[[Category: Peroxidase]]
-[[Category: Transport]]