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2q16

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[[Image:2q16.jpg|left|200px]]
 
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==Structure of the E. coli inosine triphosphate pyrophosphatase RgdB in complex with ITP==
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The line below this paragraph, containing "STRUCTURE_2q16", creates the "Structure Box" on the page.
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<StructureSection load='2q16' size='340' side='right'caption='[[2q16]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2q16]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q16 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q16 FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.95&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ITT:INOSINE+5-TRIPHOSPHATE'>ITT</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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{{STRUCTURE_2q16| PDB=2q16 | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2q16 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q16 OCA], [https://pdbe.org/2q16 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q16 RCSB], [https://www.ebi.ac.uk/pdbsum/2q16 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q16 ProSAT]</span></td></tr>
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</table>
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'''Structure of the E. coli inosine triphosphate pyrophosphatase RgdB in complex with ITP'''
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== Function ==
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[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>
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== Evolutionary Conservation ==
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==Overview==
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[[Image:Consurf_key_small.gif|200px|right]]
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Inosine triphosphate pyrophosphatases, which are ubiquitous house-cleaning enzymes, hydrolyze noncanonical nucleoside triphosphates (inosine triphosphate (ITP) and xanthosine triphosphate (XTP)) and prevent the incorporation of hypoxanthine or xanthine into nascent DNA or RNA. Here we present the 1.5-A-resolution crystal structure of the inosine triphosphate pyrophosphatase RdgB from Escherichia coli in a free state and in complex with a substrate (ITP+Ca(2+)) or a product (inosine monophosphate (IMP)). ITP binding to RdgB induced a large displacement of the alpha1 helix, closing the enzyme active site. This positions the conserved Lys13 close to the bridging oxygen between the alpha- and beta-phosphates of the substrate, weakening the P(alpha)-O bond. On the other side of the substrate, the conserved Asp69 is proposed to act as a base coordinating the catalytic water molecule. Our data provide insight into the molecular mechanisms of the substrate selectivity and catalysis of RdgB and other ITPases.
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Check<jmol>
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<jmolCheckbox>
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==About this Structure==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q1/2q16_consurf.spt"</scriptWhenChecked>
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2Q16 is a [[Single protein]] 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=2Q16 OCA].
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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==Reference==
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</jmolCheckbox>
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Molecular basis of the antimutagenic activity of the house-cleaning inosine triphosphate pyrophosphatase RdgB from Escherichia coli., Savchenko A, Proudfoot M, Skarina T, Singer A, Litvinova O, Sanishvili R, Brown G, Chirgadze N, Yakunin AF, J Mol Biol. 2007 Dec 7;374(4):1091-103. Epub 2007 Oct 11. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17976651 17976651]
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</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=2q16 ConSurf].
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[[Category: Escherichia coli]]
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<div style="clear:both"></div>
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[[Category: Nucleoside-triphosphate diphosphatase]]
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== References ==
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[[Category: Single protein]]
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<references/>
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[[Category: Lam, R.]]
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__TOC__
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[[Category: Proudfoot, M.]]
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</StructureSection>
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[[Category: Savchenko, A.]]
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[[Category: Escherichia coli K-12]]
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[[Category: Singer, A U.]]
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[[Category: Large Structures]]
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[[Category: Skarina, T.]]
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[[Category: Lam R]]
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[[Category: Yakunin, A F.]]
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[[Category: Proudfoot M]]
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[[Category: Hydrolase]]
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[[Category: Savchenko A]]
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[[Category: Itp pyrophosphatase x-ray structure enzyme mechanism substrate]]
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[[Category: Singer AU]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 14:09:19 2008''
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[[Category: Skarina T]]
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[[Category: Yakunin AF]]

Current revision

Structure of the E. coli inosine triphosphate pyrophosphatase RgdB in complex with ITP

PDB ID 2q16

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