1umj: Difference between revisions

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-[[Image:1umj.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1umj", creates the "Structure Box" on the page.
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-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
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-{{STRUCTURE_1umj|  PDB=1umj  |  SCENE=  }}
-'''Crystal structure of Pyrococcus horikoshii CutA in the presence of 3M guanidine hydrochloride'''
+==Crystal structure of Pyrococcus horikoshii CutA in the presence of 3M guanidine hydrochloride==
+<StructureSection load='1umj' size='340' side='right'caption='[[1umj]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1umj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UMJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UMJ 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]] 1.6&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GAI:GUANIDINE'>GAI</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=1umj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1umj OCA], [https://pdbe.org/1umj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1umj RCSB], [https://www.ebi.ac.uk/pdbsum/1umj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1umj ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CUTA_PYRHO CUTA_PYRHO] Involved in resistance toward heavy metals.
+== 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/um/1umj_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=1umj ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+This study was carried out to investigate the structural perturbation of the protein's local structure by the denaturants under non-denaturing conditions. Crystal structure of CutA from an archaeon Pyrococcus horikosii (PhoCutA), a heavy-metal binding protein, was determined at 1.6-angstroms resolution in the presence of 3 M guanidine HCl (GdnHCl). Native PhoCutA has a large number of short intramolecular hydrogen bonds and salt bridges on the protein surface, of which greater than 90% of hydrogen bonds and all salt bridges were retained in 3 M GdnHCl. Hydrogen bonds that disappeared in the GdnHCl crystal structure were mainly located on the protein surface, especially around the structurally perturbed loop, suggesting interactions between peptide groups and GdnHCl. Only a few GdnH+ ions were observed in the crystal structure, although none at the surface, of the protein. Two GdnH+ ions were observed in the center of the trimeric structure, replacing water molecules, and were hydrogen bonded with Asp84 and Asp86 of each chain. The exterior loop from Tyr39 to Lys44, including Trp40-Trp41, was perturbed structurally. Decreases in temperature factors were observed in beta strand 5 and the N terminus of helix 3. These results suggest the specific bindings of GdnH+ with some acidic residues and the non-specific bindings around Trp residues and peptide groups on the protein surface and that binding of GdnHCl to the native protein is limited, resulting in local structural perturbation.
-==Overview==
+Structural evidence for guanidine-protein side chain interactions: crystal structure of CutA from Pyrococcus horikoshii in 3 M guanidine hydrochloride.,Tanaka Y, Tsumoto K, Umetsu M, Nakanishi T, Yasutake Y, Sakai N, Yao M, Tanaka I, Arakawa T, Kumagai I Biochem Biophys Res Commun. 2004 Oct 8;323(1):185-91. PMID:15351719<ref>PMID:15351719</ref>
-This study was carried out to investigate the structural perturbation of the protein's local structure by the denaturants under non-denaturing conditions. Crystal structure of CutA from an archaeon Pyrococcus horikosii (PhoCutA), a heavy-metal binding protein, was determined at 1.6-angstroms resolution in the presence of 3 M guanidine HCl (GdnHCl). Native PhoCutA has a large number of short intramolecular hydrogen bonds and salt bridges on the protein surface, of which greater than 90% of hydrogen bonds and all salt bridges were retained in 3 M GdnHCl. Hydrogen bonds that disappeared in the GdnHCl crystal structure were mainly located on the protein surface, especially around the structurally perturbed loop, suggesting interactions between peptide groups and GdnHCl. Only a few GdnH+ ions were observed in the crystal structure, although none at the surface, of the protein. Two GdnH+ ions were observed in the center of the trimeric structure, replacing water molecules, and were hydrogen bonded with Asp84 and Asp86 of each chain. The exterior loop from Tyr39 to Lys44, including Trp40-Trp41, was perturbed structurally. Decreases in temperature factors were observed in beta strand 5 and the N terminus of helix 3. These results suggest the specific bindings of GdnH+ with some acidic residues and the non-specific bindings around Trp residues and peptide groups on the protein surface and that binding of GdnHCl to the native protein is limited, resulting in local structural perturbation.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-UMJ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UMJ OCA].
+</div>
+<div class="pdbe-citations 1umj" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Structural evidence for guanidine-protein side chain interactions: crystal structure of CutA from Pyrococcus horikoshii in 3 M guanidine hydrochloride., Tanaka Y, Tsumoto K, Umetsu M, Nakanishi T, Yasutake Y, Sakai N, Yao M, Tanaka I, Arakawa T, Kumagai I, Biochem Biophys Res Commun. 2004 Oct 8;323(1):185-91. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15351719 15351719]
+*[[CutA1 3D structures|CutA1 3D structures]]
-[[Category: Pyrococcus horikoshii]]
+== References ==
-[[Category: Single protein]]
+<references/>
-[[Category: Kumagai, I.]]
+__TOC__
-[[Category: Sakai, N.]]
+</StructureSection>
-[[Category: Tanaka, I.]]
+[[Category: Large Structures]]
-[[Category: Tanaka, Y.]]
+[[Category: Pyrococcus horikoshii OT3]]
-[[Category: Tsumoto, K.]]
+[[Category: Kumagai I]]
-[[Category: Yao, M.]]
+[[Category: Sakai N]]
-[[Category: Yasutake, Y.]]
+[[Category: Tanaka I]]
-[[Category: Copper tolerance]]
+[[Category: Tanaka Y]]
-[[Category: Cuta]]
+[[Category: Tsumoto K]]
-[[Category: Structural genomic]]
+[[Category: Yao M]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 11:25:40 2008''
+[[Category: Yasutake Y]]