2ciw: Difference between revisions

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-[[Image:2ciw.gif|left|200px]]
- {{Structure
+==Chloroperoxidase iodide complex==
-|PDB= 2ciw |SIZE=350|CAPTION= <scene name='initialview01'>2ciw</scene>, resolution 1.15&Aring;
+<StructureSection load='2ciw' size='340' side='right'caption='[[2ciw]], [[Resolution|resolution]] 1.15&Aring;' scene=''>
-|SITE= <scene name='pdbsite=AC1:Iod+Binding+Site+For+Chain+A'>AC1</scene>
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene>
+<table><tr><td colspan='2'>[[2ciw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Leptoxyphium_fumago Leptoxyphium fumago]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CIW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CIW FirstGlance]. <br>
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Chloride_peroxidase Chloride peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.10 1.11.1.10] </span>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.15&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene>, <scene name='pdbligand=PRD_900111:2alpha-alpha-mannobiose'>PRD_900111</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ciw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ciw OCA], [https://pdbe.org/2ciw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ciw RCSB], [https://www.ebi.ac.uk/pdbsum/2ciw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ciw ProSAT]</span></td></tr>
-|RELATEDENTRY=
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ciw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ciw OCA], [http://www.ebi.ac.uk/pdbsum/2ciw PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2ciw RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/PRXC_LEPFU PRXC_LEPFU] Catalyzes peroxidative halogenations involved in the biosynthesis of clardariomycin (2,2-dichloro-1,3-cyclo-pentenedione). The enzyme also has potent catalase activity and in the absence of halide ion, acts as a peroxidase similar to plant peroxidases.
+== 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/ci/2ciw_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2ciw ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Chloroperoxidase (CPO) is a heme-thiolate enzyme that catalyzes hydrogen peroxide-dependent halogenation reactions. Structural data on substrate binding have not been available so far. CPO was therefore crystallized in the presence of iodide or bromide. One halide binding site was identified at the surface near a narrow channel that connects the surface with the heme. Two other halide binding sites were identified within and at the other end of this channel. Together, these sites suggest a pathway for access of halide anions to the active site. The structure of CPO complexed with its natural substrate cyclopentanedione was determined at a resolution of 1.8 A. This is the first example of a CPO structure with a bound organic substrate. In addition, structures of CPO bound with nitrate, acetate, and formate and of a ternary complex with dimethylsulfoxide (Me2SO) and cyanide were determined. These structures have implications for the mechanism of compound I formation. Before binding to the heme, the incoming hydrogen peroxide first interacts with Glu-183. The deprotonated Glu-183 abstracts a proton from hydrogen peroxide. The hydroperoxo-anion then binds at the heme, yielding compound 0. Glu-183 protonates the distal oxygen of compound 0, water is released, and compound I is formed.
-'''CHLOROPEROXIDASE IODIDE COMPLEX'''
+Crystal structures of chloroperoxidase with its bound substrates and complexed with formate, acetate, and nitrate.,Kuhnel K, Blankenfeldt W, Terner J, Schlichting I J Biol Chem. 2006 Aug 18;281(33):23990-8. Epub 2006 Jun 20. PMID:16790441<ref>PMID:16790441</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2ciw" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-Chloroperoxidase (CPO) is a heme-thiolate enzyme that catalyzes hydrogen peroxide-dependent halogenation reactions. Structural data on substrate binding have not been available so far. CPO was therefore crystallized in the presence of iodide or bromide. One halide binding site was identified at the surface near a narrow channel that connects the surface with the heme. Two other halide binding sites were identified within and at the other end of this channel. Together, these sites suggest a pathway for access of halide anions to the active site. The structure of CPO complexed with its natural substrate cyclopentanedione was determined at a resolution of 1.8 A. This is the first example of a CPO structure with a bound organic substrate. In addition, structures of CPO bound with nitrate, acetate, and formate and of a ternary complex with dimethylsulfoxide (Me2SO) and cyanide were determined. These structures have implications for the mechanism of compound I formation. Before binding to the heme, the incoming hydrogen peroxide first interacts with Glu-183. The deprotonated Glu-183 abstracts a proton from hydrogen peroxide. The hydroperoxo-anion then binds at the heme, yielding compound 0. Glu-183 protonates the distal oxygen of compound 0, water is released, and compound I is formed.
+*[[Haloperoxidase|Haloperoxidase]]
+== References ==
-==About this Structure==
+<references/>
-CIW is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Leptoxyphium_fumago Leptoxyphium fumago]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CIW OCA].
+__TOC__
+</StructureSection>
-==Reference==
+[[Category: Large Structures]]
-Crystal structures of chloroperoxidase with its bound substrates and complexed with formate, acetate, and nitrate., Kuhnel K, Blankenfeldt W, Terner J, Schlichting I, J Biol Chem. 2006 Aug 18;281(33):23990-8. Epub 2006 Jun 20. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16790441 16790441]
-[[Category: Chloride peroxidase]]
 [[Category: Leptoxyphium fumago]]
-[[Category: Single protein]]
+[[Category: Blankenfeldt W]]
-[[Category: Blankenfeldt, W.]]
+[[Category: Kuhnel K]]
-[[Category: Kuhnel, K.]]
+[[Category: Schlichting I]]
-[[Category: Schlichting, I.]]
+[[Category: Terner J]]
-[[Category: Terner, J.]]
-[[Category: chloride]]
-[[Category: glycoprotein]]
-[[Category: heme]]
-[[Category: iron]]
-[[Category: manganese]]
-[[Category: metal-binding]]
-[[Category: oxidoreductase]]
-[[Category: peroxidase]]
-[[Category: pyrrolidone carboxylic acid]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:22:08 2008''