2cwq: Difference between revisions

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-{{Seed}}
-[[Image:2cwq.png|left|200px]]
-<!--
+==Crystal structure of conserved protein TTHA0727 from Thermus thermophilus HB8==
-The line below this paragraph, containing "STRUCTURE_2cwq", creates the "Structure Box" on the page.
+<StructureSection load='2cwq' size='340' side='right'caption='[[2cwq]], [[Resolution|resolution]] 1.90&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'>[[2cwq]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CWQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CWQ 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]] 1.9&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-{{STRUCTURE_2cwq|  PDB=2cwq  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2cwq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cwq OCA], [https://pdbe.org/2cwq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cwq RCSB], [https://www.ebi.ac.uk/pdbsum/2cwq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cwq ProSAT], [https://www.topsan.org/Proteins/RSGI/2cwq TOPSAN]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q5SMF5_THET8 Q5SMF5_THET8]
+== 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/cw/2cwq_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=2cwq ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+TTHA0727 is a conserved hypothetical protein from Thermus thermophilus HB8, with a molecular mass of 12.6 kDa. TTHA0727 belongs to the carboxymuconolactone decarboxylase (CMD) family (Pfam 02627). A sequence comparison with its homologs suggested that TTHA0727 is a distinct protein from alkylhydroperoxidase AhpD and gamma-carboxymuconolactone decarboxylase in the CMD family. Here we report the 1.9 A crystal structure of TTHA0727 (PDB ID: 2CWQ) determined by the multiwavelength anomalous dispersion method. The TTHA0727 monomer structure consists of seven alpha-helices (alpha1-alpha7) and one short 3(10)-helix. The crystal structure and the analytical ultracentrifugation revealed that TTHA0727 forms a hexameric ring structure in solution. The electrostatic potential distribution on the solvent-accessible surface of the TTHA0727 hexamer showed that positively charged regions exist on the side of the ring structure, suggesting that TTHA0727 interacts with some negatively charged molecules. A structural homology search revealed that the structure of three alpha-helices (alpha4-alpha6) is remarkably conserved, suggesting that it is the common structural motif for the CMD family proteins. In addition, the nine residues of the N-terminal tag bound to the cleft region between alpha1 and alpha3 in chains A and B of TTHA0727, implying that this region is the putative binding/active site for some small molecules.
-===Crystal structure of conserved protein TTHA0727 from Thermus thermophilus HB8===
+Crystal structure of the conserved protein TTHA0727 from Thermus thermophilus HB8 at 1.9 A resolution: A CMD family member distinct from carboxymuconolactone decarboxylase (CMD) and AhpD.,Ito K, Arai R, Fusatomi E, Kamo-Uchikubo T, Kawaguchi S, Akasaka R, Terada T, Kuramitsu S, Shirouzu M, Yokoyama S Protein Sci. 2006 May;15(5):1187-92. Epub 2006 Apr 5. PMID:16597838<ref>PMID:16597838</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_16597838}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2cwq" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 16597838 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16597838}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-CWQ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CWQ OCA].
+[[Category: Thermus thermophilus HB8]]
+[[Category: Arai R]]
-==Reference==
+[[Category: Fusatomi E]]
-Crystal structure of the conserved protein TTHA0727 from Thermus thermophilus HB8 at 1.9 A resolution: A CMD family member distinct from carboxymuconolactone decarboxylase (CMD) and AhpD., Ito K, Arai R, Fusatomi E, Kamo-Uchikubo T, Kawaguchi S, Akasaka R, Terada T, Kuramitsu S, Shirouzu M, Yokoyama S, Protein Sci. 2006 May;15(5):1187-92. Epub 2006 Apr 5. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16597838 16597838]
+[[Category: Ito K]]
-[[Category: Single protein]]
+[[Category: Kamo-Uchikubo T]]
-[[Category: Thermus thermophilus]]
+[[Category: Kawaguchi S]]
-[[Category: Arai, R.]]
+[[Category: Shirouzu M]]
-[[Category: Fusatomi, E.]]
+[[Category: Terada T]]
-[[Category: Ito, K.]]
+[[Category: Yokoyama S]]
-[[Category: Kamo-Uchikubo, T.]]
-[[Category: Kawaguchi, S.]]
-[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
-[[Category: Shirouzu, M.]]
-[[Category: Terada, T.]]
-[[Category: Yokoyama, S.]]
-[[Category: All alpha]]
-[[Category: Conserved hypothetical protein]]
-[[Category: National project on protein structural and functional analyse]]
-[[Category: Nppsfa]]
-[[Category: Riken structural genomics/proteomics initiative]]
-[[Category: Rsgi]]
-[[Category: Structural genomic]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 15:01:31 2008''