1k7k: Difference between revisions

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-{{Seed}}
-[[Image:1k7k.png|left|200px]]
-<!--
+==crystal structure of RdgB- inosine triphosphate pyrophosphatase from E. coli==
-The line below this paragraph, containing "STRUCTURE_1k7k", creates the "Structure Box" on the page.
+<StructureSection load='1k7k' size='340' side='right'caption='[[1k7k]], [[Resolution|resolution]] 1.50&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'>[[1k7k]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K7K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K7K 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]] 1.5&#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_1k7k|  PDB=1k7k  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1k7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k7k OCA], [https://pdbe.org/1k7k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k7k RCSB], [https://www.ebi.ac.uk/pdbsum/1k7k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k7k ProSAT], [https://www.topsan.org/Proteins/MCSG/1k7k TOPSAN]</span></td></tr>
+</table>
-===crystal structure of RdgB- inosine triphosphate pyrophosphatase from E. coli===
+== Function ==
+[https://www.uniprot.org/uniprot/IXTPA_ECOLI IXTPA_ECOLI] Pyrophosphatase that catalyzes the hydrolysis of nucleoside triphosphates to their monophosphate derivatives, with a high preference for the non-canonical purine nucleotides XTP (xanthosine triphosphate), dITP (deoxyinosine triphosphate) and ITP (PubMed:12297000, PubMed:17976651). Can also efficiently hydrolyze 2'-deoxy-N-6-hydroxylaminopurine triphosphate (dHAPTP) (PubMed:17090528). Seems to function as a house-cleaning enzyme that removes non-canonical purine nucleotides from the nucleotide pool, thus preventing their incorporation into DNA/RNA and avoiding chromosomal lesions (PubMed:12297000, PubMed:12730170, PubMed:17090528). To a much lesser extent, is also able to hydrolyze GTP, dGTP and dUTP, but shows very low activity toward the canonical nucleotides dATP, dCTP and dTTP and toward 8-oxo-dGTP, purine deoxyribose triphosphate, 2-aminopurine deoxyribose triphosphate and 2,6-diaminopurine deoxyribose triphosphate (PubMed:12297000, PubMed:17090528).[HAMAP-Rule:MF_01405]<ref>PMID:12297000</ref> <ref>PMID:12730170</ref> <ref>PMID:17090528</ref> <ref>PMID:17976651</ref>
+== Evolutionary Conservation ==
-==About this Structure==
+[[Image:Consurf_key_small.gif|200px|right]]
-K7K is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K7K OCA].
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k7/1k7k_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=1k7k ConSurf].
+<div style="clear:both"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Edwards, A.]]
+[[Category: Large Structures]]
-[[Category: Joachimiak, A.]]
+[[Category: Edwards A]]
-[[Category: MCSG, Midwest Center for Structural Genomics.]]
+[[Category: Joachimiak A]]
-[[Category: Sanishvili, R.]]
+[[Category: Sanishvili R]]
-[[Category: Savchenko, A.]]
+[[Category: Savchenko A]]
-[[Category: Skarina, T.]]
+[[Category: Skarina T]]
-[[Category: Disordered se-met]]
-[[Category: His-tag]]
-[[Category: Large groove]]
-[[Category: Mad]]
-[[Category: Mcsg]]
-[[Category: Midwest center for structural genomic]]
-[[Category: Protein structure initiative]]
-[[Category: Psi]]
-[[Category: Putative ribosomal protein]]
-[[Category: Structural genomic]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Nov 16 11:56:59 2008''