1puq: Difference between revisions

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New page: left|200px<br /><applet load="1puq" size="450" color="white" frame="true" align="right" spinBox="true" caption="1puq" /> '''Solution Structure of the MutT Pyrophosphohy...
 
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[[Image:1puq.gif|left|200px]]<br /><applet load="1puq" size="450" color="white" frame="true" align="right" spinBox="true"
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'''Solution Structure of the MutT Pyrophosphohydrolase Complexed with Mg(2+) and 8-oxo-dGMP, a Tightly-bound Product'''<br />


==Overview==
==Solution Structure of the MutT Pyrophosphohydrolase Complexed with Mg(2+) and 8-oxo-dGMP, a Tightly-bound Product==
To learn the structural basis for the unusually tight binding of, 8-oxo-nucleotides to the MutT pyrophosphohydrolase of Escherichia coli, (129 residues), the solution structure of the MutT-Mg(2+)-8-oxo-dGMP, product complex (K(D) = 52 nM) was determined by standard 3-D, heteronuclear NMR methods. Using 1746 NOEs (13.5 NOEs/residue) and 186 phi, and psi values derived from backbone (15)N, Calpha, Halpha, and Cbeta, chemical shifts, 20 converged structures were computed with NOE violations, &lt;or=0.25 A and total energies &lt;or=450 kcal/mol. The pairwise, root-mean-square deviations (RMSD) of backbone N, Calpha, and C' atoms for, the secondary structured regions and for all residues of the 20 structures, are 0.65 and 0.98 A, respectively, indicating a well-defined structure., Further refinement using residual dipolar coupling from 53 backbone N-H, vectors slightly improved the RMSD values to 0.49 and 0.84 A, respectively. The secondary structures, which consisted of two, alpha-helices and a five-stranded mixed beta-sheet, were indistinguishable, from those of free MutT and of MutT in the quaternary, MutT-Mg(2+)-(H(2)O)-AMPCPP-Mg(2+) complex. Comparisons of these three, tertiary structures showed a narrowing of the hydrophobic, nucleotide-binding cleft in the 8-oxo-dGMP complex resulting from a, 2.5-4.5 A movement of helix I and a 1.5 A movement of helix II and loop 4, toward the cleft. The binding of 8-oxo-dGMP to MutT-Mg(2+) buries 71-78%, of the surface area of the nucleotide. The 10(3.7)-fold weaker binding, substrate analogue Mg(2+)-AMPCPP induced much smaller changes in tertiary, structure, and MutT buried only 57% of the surface of the AMP moiety of, AMPCPP. Formation of the MutT-Mg(2+)-8-oxo-dGMP complex slowed the, backbone NH exchange rates of 45 residues of the enzyme by factors of, 10(1)-10(6) as compared with the MutT-Mg(2+) and the MutT-Mg(2+)-dGMP, complexes, suggesting a more compact structure when 8-oxo-dGMP is bound., The 10(4.6)-fold weaker binding of dGMP to MutT-Mg(2+) (K(D) = 1.8 mM), slowed the backbone exchange rates of only 20 residues and by smaller, factors of approximately 10. Hence, the high affinity of MutT-Mg(2+) for, 8-oxo-dGMP likely results from widespread ligand-induced conformation, changes that narrow the nucleotide binding site and lower the overall free, energy of the enzyme-product complex. Specific hydrogen bonding of the, purine ring of 8-oxo-dGMP by the side chains of Asn-119 and Arg-78 may, also contribute.
<StructureSection load='1puq' size='340' side='right'caption='[[1puq]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1puq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PUQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PUQ FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=1puq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1puq OCA], [https://pdbe.org/1puq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1puq RCSB], [https://www.ebi.ac.uk/pdbsum/1puq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1puq ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/MUTT_ECOLI MUTT_ECOLI] Involved in the GO system responsible for removing an oxidatively damaged form of guanine (7,8-dihydro-8-oxoguanine) from DNA and the nucleotide pool. 8-oxo-dGTP is inserted opposite dA and dC residues of template DNA with almost equal efficiency thus leading to A.T to G.C transversions. MutT specifically degrades 8-oxo-dGTP to the monophosphate.<ref>PMID:1309939</ref> <ref>PMID:15850400</ref>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pu/1puq_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=1puq ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1PUQ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with MG and 8OG as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1PUQ OCA].
*[[7%2C8-dihydro-8-oxoguanine triphosphatase 3D structures|7%2C8-dihydro-8-oxoguanine triphosphatase 3D structures]]
 
== References ==
==Reference==
<references/>
Solution structure and NH exchange studies of the MutT pyrophosphohydrolase complexed with Mg(2+) and 8-oxo-dGMP, a tightly bound product., Massiah MA, Saraswat V, Azurmendi HF, Mildvan AS, Biochemistry. 2003 Sep 2;42(34):10140-54. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12939141 12939141]
__TOC__
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Azurmendi, H.F.]]
[[Category: Azurmendi HF]]
[[Category: Massiah, M.A.]]
[[Category: Massiah MA]]
[[Category: Mildvan, A.S.]]
[[Category: Mildvan AS]]
[[Category: Saraswat, V.]]
[[Category: Saraswat V]]
[[Category: 8OG]]
[[Category: MG]]
[[Category: mutator protein]]
[[Category: mutt pyrophosphohydrolase-metal-product complex]]
[[Category: nucleoside triphosphate pyrophosphohydrolase]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 00:08:15 2007''

Latest revision as of 08:59, 17 April 2024

Solution Structure of the MutT Pyrophosphohydrolase Complexed with Mg(2+) and 8-oxo-dGMP, a Tightly-bound ProductSolution Structure of the MutT Pyrophosphohydrolase Complexed with Mg(2+) and 8-oxo-dGMP, a Tightly-bound Product

Structural highlights

1puq is a 1 chain structure with sequence from Escherichia coli. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Solution NMR
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MUTT_ECOLI Involved in the GO system responsible for removing an oxidatively damaged form of guanine (7,8-dihydro-8-oxoguanine) from DNA and the nucleotide pool. 8-oxo-dGTP is inserted opposite dA and dC residues of template DNA with almost equal efficiency thus leading to A.T to G.C transversions. MutT specifically degrades 8-oxo-dGTP to the monophosphate.[1] [2]

Evolutionary Conservation

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

See Also

References

  1. ↑ Maki H, Sekiguchi M. MutT protein specifically hydrolyses a potent mutagenic substrate for DNA synthesis. Nature. 1992 Jan 16;355(6357):273-5. PMID:1309939 doi:http://dx.doi.org/10.1038/355273a0
  2. ↑ Ito R, Hayakawa H, Sekiguchi M, Ishibashi T. Multiple enzyme activities of Escherichia coli MutT protein for sanitization of DNA and RNA precursor pools. Biochemistry. 2005 May 3;44(17):6670-4. PMID:15850400 doi:http://dx.doi.org/10.1021/bi047550k
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