2q16: Difference between revisions

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<StructureSection load='2q16' size='340' side='right'caption='[[2q16]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
<StructureSection load='2q16' size='340' side='right'caption='[[2q16]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2q16]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. 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>
<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>
</td></tr><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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
</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>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
<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>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1k7k|1k7k]], [[2pyu|2pyu]]</div></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">yggV ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Nucleoside-triphosphate_diphosphatase Nucleoside-triphosphate diphosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.19 3.6.1.19] </span></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=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>
<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>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/RDGB_ECOLI RDGB_ECOLI]] Pyrophosphatase that hydrolyzes the non-canonical purine nucleotides deoxyinosine triphosphate (dITP) and xanthosine triphosphate (XTP) as well as 2'-deoxy-N-6-hydroxylaminopurine triposphate (dHAPTP) to their respective monophosphate derivatives. Probably excludes non-canonical purines from DNA precursor pool, thus preventing their incorporation into DNA and avoiding chromosomal lesions.[HAMAP-Rule:MF_01405]<ref>PMID:17090528</ref>
[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 ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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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].
</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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<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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:17976651<ref>PMID:17976651</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2q16" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Ecoli]]
[[Category: Escherichia coli K-12]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Nucleoside-triphosphate diphosphatase]]
[[Category: Lam R]]
[[Category: Lam, R]]
[[Category: Proudfoot M]]
[[Category: Proudfoot, M]]
[[Category: Savchenko A]]
[[Category: Savchenko, A]]
[[Category: Singer AU]]
[[Category: Singer, A U]]
[[Category: Skarina T]]
[[Category: Skarina, T]]
[[Category: Yakunin AF]]
[[Category: Yakunin, A F]]
[[Category: Hydrolase]]
[[Category: Itp pyrophosphatase x-ray structure enzyme mechanism substrate]]
Retrieved from "https://proteopedia.org/2q16"