1k0i: Difference between revisions

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-{{Seed}}
-[[Image:1k0i.png|left|200px]]
-<!--
+==Pseudomonas aeruginosa phbh R220Q in complex with 100mM PHB==
-The line below this paragraph, containing "STRUCTURE_1k0i", creates the "Structure Box" on the page.
+<StructureSection load='1k0i' size='340' side='right'caption='[[1k0i]], [[Resolution|resolution]] 1.80&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'>[[1k0i]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K0I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K0I 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]] 1.8&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=PHB:P-HYDROXYBENZOIC+ACID'>PHB</scene>, <scene name='pdbligand=SO3:SULFITE+ION'>SO3</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_1k0i|  PDB=1k0i  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1k0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k0i OCA], [https://pdbe.org/1k0i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k0i RCSB], [https://www.ebi.ac.uk/pdbsum/1k0i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k0i ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PHHY_PSEAE PHHY_PSEAE]
+== 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/k0/1k0i_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=1k0i ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+para-Hydroxybenzoate hydroxylase catalyzes a two-step reaction that demands precise control of solvent access to the catalytic site. The first step of the reaction, reduction of flavin by NADPH, requires access to solvent. The second step, oxygenation of reduced flavin to a flavin C4a-hydroperoxide that transfers the hydroxyl group to the substrate, requires that solvent be excluded to prevent breakdown of the hydroperoxide to oxidized flavin and hydrogen peroxide. These conflicting requirements are met by the coordination of multiple movements involving the protein, the two cofactors, and the substrate. Here, using the R220Q mutant form of para-hydroxybenzoate hydroxylase, we show that in the absence of substrate, the large beta alpha beta domain (residues 1-180) and the smaller sheet domain (residues 180-270) separate slightly, and the flavin swings out to a more exposed position to open an aqueous channel from the solvent to the protein interior. Substrate entry occurs by first binding at a surface site and then sliding into the protein interior. In our study of this mutant, the structure of the complex with pyridine nucleotide was obtained. This cofactor binds in an extended conformation at the enzyme surface in a groove that crosses the binding site of FAD. We postulate that for stereospecific reduction, the flavin swings to an out position and NADPH assumes a folded conformation that brings its nicotinamide moiety into close contact with the isoalloxazine moiety of the flavin. This work clearly shows how complex dynamics can play a central role in catalysis by enzymes.
-===Pseudomonas aeruginosa phbh R220Q in complex with 100mM PHB===
+Protein and ligand dynamics in 4-hydroxybenzoate hydroxylase.,Wang J, Ortiz-Maldonado M, Entsch B, Massey V, Ballou D, Gatti DL Proc Natl Acad Sci U S A. 2002 Jan 22;99(2):608-13. PMID:11805318<ref>PMID:11805318</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1k0i" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_11805318}}, adds the Publication Abstract to the page
+*[[Hydroxylases 3D structures|Hydroxylases 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 11805318 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_11805318}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-K0I is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K0I OCA].
-==Reference==
-Protein and ligand dynamics in 4-hydroxybenzoate hydroxylase., Wang J, Ortiz-Maldonado M, Entsch B, Massey V, Ballou D, Gatti DL, Proc Natl Acad Sci U S A. 2002 Jan 22;99(2):608-13. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11805318 11805318]
-[[Category: 4-hydroxybenzoate 3-monooxygenase]]
 [[Category: Pseudomonas aeruginosa]]
-[[Category: Single protein]]
+[[Category: Ballou D]]
-[[Category: Ballou, D.]]
+[[Category: Entsch B]]
-[[Category: Entsch, B.]]
+[[Category: Gatti DL]]
-[[Category: Gatti, D L.]]
+[[Category: Ortiz-Maldonado M]]
-[[Category: Ortiz-Maldonado, M.]]
+[[Category: Wang J]]
-[[Category: Wang, J.]]
-[[Category: Fad]]
-[[Category: Mechanism]]
-[[Category: P-ohb]]
-[[Category: Phbh]]
-[[Category: Structure]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul  1 21:10:51 2008''