2dqb: Difference between revisions

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-{{Seed}}
-[[Image:2dqb.png|left|200px]]
-<!--
+==Crystal structure of dNTP triphosphohydrolase from Thermus thermophilus HB8, which is homologous to dGTP triphosphohydrolase==
-The line below this paragraph, containing "STRUCTURE_2dqb", creates the "Structure Box" on the page.
+<StructureSection load='2dqb' size='340' side='right'caption='[[2dqb]], [[Resolution|resolution]] 2.20&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'>[[2dqb]] is a 6 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=2DQB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DQB 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]] 2.2&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-{{STRUCTURE_2dqb|  PDB=2dqb  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2dqb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dqb OCA], [https://pdbe.org/2dqb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dqb RCSB], [https://www.ebi.ac.uk/pdbsum/2dqb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dqb ProSAT], [https://www.topsan.org/Proteins/RSGI/2dqb TOPSAN]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q5SL81_THET8 Q5SL81_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/dq/2dqb_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=2dqb ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Deoxyribonucleoside triphosphate triphosphohydrolase from Thermus thermophilus (Tt-dNTPase) has a unique regulatory mechanism for the degradation of deoxyribonucleoside triphosphates (dNTPs). Whereas the Escherichia coli homologue specifically hydrolyzes dGTP alone, dNTPs act as both substrate and activator for Tt-dNTPase. Here, the crystal structure of Tt-dNTPase has been determined at 2.2 A resolution, representing the first report of the tertiary structure of a dNTPase homologue belonging to the HD superfamily, a diverse group of metal-dependent phosphohydrolases that includes a variety of uncharacterized proteins. This enzyme forms a homohexamer as a double ring of trimers. The subunit is composed of 19 alpha-helices; the inner six helices include the region annotated as the catalytic domain of the HD superfamily. Structural comparison with other HD-superfamily proteins indicates that a pocket at the centre of the inner six helices, formed from highly conserved charged residues clustered around a bound magnesium ion, constitutes the catalytic site. Tt-dNTPase also hydrolyzed noncanonical dNTPs, but hardly hydrolyzed dNDP and dNMP. The broad substrate specificity for different dNTPs might be rationalized by the involvement of a flexible loop during molecular recognition of the base moiety. Recognition of the triphosphate moiety crucial for the activity might be attained by highly conserved positively charged residues. The possible mode of dNTP binding is discussed in light of the structure.
-===Crystal structure of dNTP triphosphohydrolase from Thermus thermophilus HB8, which is homologous to dGTP triphosphohydrolase===
+Structure of dNTP-inducible dNTP triphosphohydrolase: insight into broad specificity for dNTPs and triphosphohydrolase-type hydrolysis.,Kondo N, Nakagawa N, Ebihara A, Chen L, Liu ZJ, Wang BC, Yokoyama S, Kuramitsu S, Masui R Acta Crystallogr D Biol Crystallogr. 2007 Feb;63(Pt 2):230-9. Epub 2007, Jan 16. PMID:17242516<ref>PMID:17242516</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_17242516}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2dqb" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 17242516 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17242516}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-DQB 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=2DQB OCA].
+[[Category: Thermus thermophilus HB8]]
+[[Category: Chen L]]
-==Reference==
+[[Category: Ebihara A]]
-Structure of dNTP-inducible dNTP triphosphohydrolase: insight into broad specificity for dNTPs and triphosphohydrolase-type hydrolysis., Kondo N, Nakagawa N, Ebihara A, Chen L, Liu ZJ, Wang BC, Yokoyama S, Kuramitsu S, Masui R, Acta Crystallogr D Biol Crystallogr. 2007 Feb;63(Pt 2):230-9. Epub 2007, Jan 16. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17242516 17242516]
+[[Category: Kondo N]]
-[[Category: Single protein]]
+[[Category: Kuramitsu S]]
-[[Category: Thermus thermophilus]]
+[[Category: Liu Z-J]]
-[[Category: DGTPase]]
+[[Category: Masui R]]
-[[Category: Chen, L.]]
+[[Category: Nakagawa N]]
-[[Category: Ebihara, A.]]
+[[Category: Wang B-C]]
-[[Category: Kondo, N.]]
+[[Category: Yokoyama S]]
-[[Category: Kuramitsu, S.]]
-[[Category: Liu, Z J.]]
-[[Category: Masui, R.]]
-[[Category: Nakagawa, N.]]
-[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
-[[Category: Wang, B C.]]
-[[Category: Yokoyama, S.]]
-[[Category: Dgtpase]]
-[[Category: Dna]]
-[[Category: Dntp]]
-[[Category: Dntpase]]
-[[Category: Hd superfamily]]
-[[Category: National project on protein structural and functional analyse]]
-[[Category: Nppsfa]]
-[[Category: Riken structural genomics/proteomics initiative]]
-[[Category: Rsgi]]
-[[Category: Single-stranded dna]]
-[[Category: Structural genomic]]
-[[Category: Triphosphohydrolase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 13:18:13 2008''