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[[Image:1k7k.gif|left|200px]]


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==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]]
1K7K 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=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: Escherichia coli]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Edwards, A.]]
[[Category: Edwards A]]
[[Category: Joachimiak, A.]]
[[Category: Joachimiak A]]
[[Category: MCSG, Midwest Center for Structural Genomics.]]
[[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 Fri May  2 22:24:20 2008''

Latest revision as of 10:58, 3 April 2024

crystal structure of RdgB- inosine triphosphate pyrophosphatase from E. colicrystal structure of RdgB- inosine triphosphate pyrophosphatase from E. coli

Structural highlights

1k7k is a 1 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.5Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

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][1] [2] [3] [4]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

References

  1. ↑ Chung JH, Park HY, Lee JH, Jang Y. Identification of the dITP J Biochem Mol Biol. 2002 Jul 31;35(4):403-8. PMID:12297000 doi:10.5483/bmbrep.2002.35.4.403
  2. ↑ Burgis NE, Brucker JJ, Cunningham RP. Repair system for noncanonical purines in Escherichia coli. J Bacteriol. 2003 May;185(10):3101-10. PMID:12730170 doi:10.1128/JB.185.10.3101-3110.2003
  3. ↑ Burgis NE, Cunningham RP. Substrate specificity of RdgB protein, a deoxyribonucleoside triphosphate pyrophosphohydrolase. J Biol Chem. 2007 Feb 9;282(6):3531-8. Epub 2006 Nov 6. PMID:17090528 doi:M608708200
  4. ↑ Savchenko A, Proudfoot M, Skarina T, Singer A, Litvinova O, Sanishvili R, Brown G, Chirgadze N, Yakunin AF. Molecular basis of the antimutagenic activity of the house-cleaning inosine triphosphate pyrophosphatase RdgB from Escherichia coli. J Mol Biol. 2007 Dec 7;374(4):1091-103. Epub 2007 Oct 11. PMID:17976651 doi:http://dx.doi.org/10.1016/j.jmb.2007.10.012

1k7k, resolution 1.50Å

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