1itk: Difference between revisions

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-{{Seed}}
-[[Image:1itk.png|left|200px]]
-<!--
+==Crystal structure of catalase-peroxidase from Haloarcula marismortui==
-The line below this paragraph, containing "STRUCTURE_1itk", creates the "Structure Box" on the page.
+<StructureSection load='1itk' size='340' side='right'caption='[[1itk]], [[Resolution|resolution]] 2.00&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'>[[1itk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ITK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ITK 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]] 2&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>
-{{STRUCTURE_1itk|  PDB=1itk  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1itk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1itk OCA], [https://pdbe.org/1itk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1itk RCSB], [https://www.ebi.ac.uk/pdbsum/1itk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1itk ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/KATG2_HALMA KATG2_HALMA] Bifunctional enzyme with both catalase and broad-spectrum peroxidase activity.[HAMAP-Rule:MF_01961]
+== 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/it/1itk_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=1itk ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Catalase-peroxidase is a member of the class I peroxidase superfamily. The enzyme exhibits both catalase and peroxidase activities to remove the harmful peroxide molecule from the living cell. The 2.0 A crystal structure of the catalase-peroxidase from Haloarcula marismortui (HmCP) reveals that the enzyme is a dimer of two identical subunits. Each subunit is composed of two structurally homologous domains with a topology similar to that of class I peroxidase. The active site of HmCP is in the N-terminal domain. Although the arrangement of the catalytic residues and the cofactor heme b in the active site is virtually identical to that of class I peroxidases, the heme moiety is buried inside the domain, similar to that in a typical catalase. In the vicinity of the active site, novel covalent bonds are formed among the side chains of three residues, including that of a tryptophan on the distal side of the heme. Together with the C-terminal domain, these covalent bonds fix two long loops on the surface of the enzyme that cover the substrate access channel to the active site. These features provide an explanation for the dual activities of this enzyme.
-===Crystal structure of catalase-peroxidase from Haloarcula marismortui===
+The 2.0 A crystal structure of catalase-peroxidase from Haloarcula marismortui.,Yamada Y, Fujiwara T, Sato T, Igarashi N, Tanaka N Nat Struct Biol. 2002 Sep;9(9):691-5. PMID:12172540<ref>PMID:12172540</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1itk" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_12172540}}, adds the Publication Abstract to the page
+*[[Catalase 3D structures|Catalase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 12172540 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_12172540}}
+__TOC__
+</StructureSection>
-==About this Structure==
-ITK is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ITK OCA].
-==Reference==
-The 2.0 A crystal structure of catalase-peroxidase from Haloarcula marismortui., Yamada Y, Fujiwara T, Sato T, Igarashi N, Tanaka N, Nat Struct Biol. 2002 Sep;9(9):691-5. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12172540 12172540]
-[[Category: Catalase]]
 [[Category: Haloarcula marismortui]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Fujiwara, T.]]
+[[Category: Fujiwara T]]
-[[Category: Igarashi, N.]]
+[[Category: Igarashi N]]
-[[Category: Sato, T.]]
+[[Category: Sato T]]
-[[Category: Tanaka, N.]]
+[[Category: Tanaka N]]
-[[Category: Yamada, Y.]]
+[[Category: Yamada Y]]
-[[Category: Heme protein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul  1 13:58:36 2008''