2npx: Difference between revisions

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OCA

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-[[Image:2npx.jpg|left|200px]]<br /><applet load="2npx" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="2npx, resolution 2.4&Aring;" />
-'''NADH BINDING SITE AND CATALYSIS OF NADH PEROXIDASE'''<br />
-==Overview==
+==NADH BINDING SITE AND CATALYSIS OF NADH PEROXIDASE==
-The structure of the complex between cofactor NADH and the enzyme NADH, peroxidase from Streptococcus faecalis 10C1 (Enterococcus faecalis) has, been determined by crystal soaking, X-ray data collection, model building, of NADH and refinement at 0.24-nm resolution based on the known enzyme, structure [Stehle, T., Ahmed, S. A., Claiborne, A. &amp; Schulz, G. E. (1991), J. Mol. Biol. 221, 1325-1344]. Apart from NADH, the catalytic center of, the enzyme contains FAD and a cysteine that shuttles between thiolate and, sulfenic acid states. Unfortunately, this cysteine was irreversibly, oxidized to a cysteine sulfonic acid in the established enzyme structure., Based on the geometry of the catalytic center, we discuss the, stabilization of the oxidation-sensitive sulfenic acid and propose a, reaction mechanism.
+<StructureSection load='2npx' size='340' side='right'caption='[[2npx]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2npx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterococcus_faecalis Enterococcus faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NPX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NPX 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]] 2.4&#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=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</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=2npx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2npx OCA], [https://pdbe.org/2npx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2npx RCSB], [https://www.ebi.ac.uk/pdbsum/2npx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2npx ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NAPE_ENTFA NAPE_ENTFA] Peroxidase whose active site is a redox-active cysteine-sulfenic acid.
+== 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/np/2npx_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=2npx ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The structure of the complex between cofactor NADH and the enzyme NADH peroxidase from Streptococcus faecalis 10C1 (Enterococcus faecalis) has been determined by crystal soaking, X-ray data collection, model building of NADH and refinement at 0.24-nm resolution based on the known enzyme structure [Stehle, T., Ahmed, S. A., Claiborne, A. &amp; Schulz, G. E. (1991) J. Mol. Biol. 221, 1325-1344]. Apart from NADH, the catalytic center of the enzyme contains FAD and a cysteine that shuttles between thiolate and sulfenic acid states. Unfortunately, this cysteine was irreversibly oxidized to a cysteine sulfonic acid in the established enzyme structure. Based on the geometry of the catalytic center, we discuss the stabilization of the oxidation-sensitive sulfenic acid and propose a reaction mechanism.
-==About this Structure==
+NADH binding site and catalysis of NADH peroxidase.,Stehle T, Claiborne A, Schulz GE Eur J Biochem. 1993 Jan 15;211(1-2):221-6. PMID:8425532<ref>PMID:8425532</ref>
-NPX is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Enterococcus_faecalis Enterococcus faecalis] with CYO, FAD and NAD as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/NADH_peroxidase NADH peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.1 1.11.1.1] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2NPX OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-NADH binding site and catalysis of NADH peroxidase., Stehle T, Claiborne A, Schulz GE, Eur J Biochem. 1993 Jan 15;211(1-2):221-6. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8425532 8425532]
+</div>
+<div class="pdbe-citations 2npx" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[NADH peroxidase|NADH peroxidase]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Enterococcus faecalis]]
-[[Category: NADH peroxidase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Claiborne A]]
-[[Category: Claiborne, A.]]
+[[Category: Schulz GE]]
-[[Category: Schulz, G.E.]]
+[[Category: Stehle T]]
-[[Category: Stehle, T.]]
-[[Category: CYO]]
-[[Category: FAD]]
-[[Category: NAD]]
-[[Category: oxidoreductase(h2o2(a))]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 12:50:28 2007''