1qsl: Difference between revisions

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New page: left|200px<br /><applet load="1qsl" size="450" color="white" frame="true" align="right" spinBox="true" caption="1qsl, resolution 2.20Å" /> '''KLENOW FRAGMENT COMP...
 
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[[Image:1qsl.gif|left|200px]]<br /><applet load="1qsl" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1qsl, resolution 2.20&Aring;" />
'''KLENOW FRAGMENT COMPLEXED WITH SINGLE-STRANDED SUBSTRATE AND EUROPIUM (III) ION'''<br />


==Overview==
==KLENOW FRAGMENT COMPLEXED WITH SINGLE-STRANDED SUBSTRATE AND EUROPIUM (III) ION==
BACKGROUND: Biochemical and biophysical experiments have shown that two, catalytically essential divalent metal ions (termed 'A' and 'B') bind to, the 3'-5' exonuclease active site of the Klenow fragment (KF) of, Escherichia coli DNA polymerase I. X-ray crystallographic studies have, established the normal positions in the KF 3'-5' exonuclease (KF exo), active site of the two cations and the single-stranded DNA substrate., Lanthanide (III) luminescence studies have demonstrated, however, that, only a single europium (III) ion (Eu3+) binds to the KF exo active site., Furthermore, Eu3+ does not support catalysis by KF exo or several other, two-metal-ion phosphoryl-transfer enzymes. RESULTS: A crystal structure of, KF complexed with both Eu3+ and substrate single-stranded, oligodeoxynucleotide shows that a lone Eu3+ is bound near to metal-ion, site A. Comparison of this structure to a relevant native structure, reveals that the bound Eu3+ causes a number of changes to the KF exo, active site. The scissile phosphate of the substrate is displaced from its, normal position by about 1 A when Eu3+ is bound and the presence of Eu3+, in the active site precludes the binding of the essential metal ion B., CONCLUSIONS: The substantial, lanthanide-induced differences in metal-ion, and substrate binding to KF exo account for the inhibition of this enzyme, by Eu3+. These changes also explain the inability of KF exo to bind more, than one cation in the presence of lanthanides. The mechanistic similarity, between KF exo and other two-metal-ion phosphoryl-transfer enzymes, suggests that the principles of lanthanide (III) ion binding and, inhibition ascertained from this study will probably apply to most members, of this class of enzymes.
<StructureSection load='1qsl' size='340' side='right'caption='[[1qsl]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1qsl]] is a 2 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=1QSL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QSL FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EU:EUROPIUM+ION'>EU</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=1qsl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qsl OCA], [https://pdbe.org/1qsl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qsl RCSB], [https://www.ebi.ac.uk/pdbsum/1qsl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qsl ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DPO1_ECOLI DPO1_ECOLI] In addition to polymerase activity, this DNA polymerase exhibits 3' to 5' and 5' to 3' exonuclease activity. It is able to utilize nicked circular duplex DNA as a template and can unwind the parental DNA strand from its template.
== 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/qs/1qsl_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=1qsl ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1QSL 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 EU as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1QSL OCA].
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Structural elucidation of the binding and inhibitory properties of lanthanide (III) ions at the 3'-5' exonucleolytic active site of the Klenow fragment., Brautigam CA, Aschheim K, Steitz TA, Chem Biol. 1999 Dec;6(12):901-8. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10631518 10631518]
[[Category: DNA-directed DNA polymerase]]
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Aschheim, K.]]
[[Category: Aschheim K]]
[[Category: Brautigam, C.A.]]
[[Category: Brautigam CA]]
[[Category: Steitz, T.A.]]
[[Category: Steitz TA]]
[[Category: EU]]
[[Category: exonuclease]]
[[Category: single-stranded dna]]
[[Category: transferase/dna]]
[[Category: two metal ions]]
 
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Latest revision as of 08:17, 14 February 2024

KLENOW FRAGMENT COMPLEXED WITH SINGLE-STRANDED SUBSTRATE AND EUROPIUM (III) ION

1qsl, resolution 2.20Å

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