2pyu: Difference between revisions
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==Structure of the E. coli inosine triphosphate pyrophosphatase RgdB in complex with IMP== | ==Structure of the E. coli inosine triphosphate pyrophosphatase RgdB in complex with IMP== | ||
<StructureSection load='2pyu' size='340' side='right' caption='[[2pyu]], [[Resolution|resolution]] 2.02Å' scene=''> | <StructureSection load='2pyu' size='340' side='right'caption='[[2pyu]], [[Resolution|resolution]] 2.02Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2pyu]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[2pyu]] is a 1 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=2PYU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PYU FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.02Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IMP:INOSINIC+ACID'>IMP</scene></td></tr> | |||
<tr id=' | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2pyu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pyu OCA], [https://pdbe.org/2pyu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pyu RCSB], [https://www.ebi.ac.uk/pdbsum/2pyu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pyu ProSAT]</span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | == 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 == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/py/2pyu_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/py/2pyu_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </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/ | </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=2pyu ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
| Line 34: | Line 33: | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Escherichia coli K-12]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Proudfoot | [[Category: Proudfoot M]] | ||
[[Category: Savchenko | [[Category: Savchenko A]] | ||
[[Category: Singer | [[Category: Singer AU]] | ||
[[Category: Skarina | [[Category: Skarina T]] | ||
[[Category: Yakunin | [[Category: Yakunin AF]] | ||
