1qum

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(New page: 200px<br /><applet load="1qum" size="450" color="white" frame="true" align="right" spinBox="true" caption="1qum, resolution 1.55&Aring;" /> '''CRYSTAL STRUCTURE OF...)
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[[Image:1qum.gif|left|200px]]<br /><applet load="1qum" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1qum, resolution 1.55&Aring;" />
 
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'''CRYSTAL STRUCTURE OF ESCHERICHIA COLI ENDONUCLEASE IV IN COMPLEX WITH DAMAGED DNA'''<br />
 
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==Overview==
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==CRYSTAL STRUCTURE OF ESCHERICHIA COLI ENDONUCLEASE IV IN COMPLEX WITH DAMAGED DNA==
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Endonuclease IV is the archetype for a conserved apurinic/apyrimidinic, (AP) endonuclease family that primes DNA repair synthesis by cleaving the, DNA backbone 5' of AP sites. The crystal structures of Endonuclease IV and, its AP-DNA complex at 1.02 and 1.55 A resolution reveal how an alpha8beta8, TIM barrel fold can bind dsDNA. Enzyme loops intercalate side chains at, the abasic site, compress the DNA backbone, bend the DNA approximately 90, degrees, and promote double-nucleotide flipping to sequester the, extrahelical AP site in an enzyme pocket that excludes undamaged, nucleotides. These structures suggest three Zn2+ ions directly participate, in phosphodiester bond cleavage and prompt hypotheses that, double-nucleotide flipping and sharp bending by AP endonucleases provide, exquisite damage specificity while aiding subsequent base excision repair, pathway progression.
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<StructureSection load='1qum' size='340' side='right'caption='[[1qum]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1qum]] is a 4 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=1QUM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QUM FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.55&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1qum FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qum OCA], [https://pdbe.org/1qum PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qum RCSB], [https://www.ebi.ac.uk/pdbsum/1qum PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qum ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/END4_ECOLI END4_ECOLI] Endonuclease IV plays a role in DNA repair. It cleaves phosphodiester bonds at apurinic or apyrimidinic sites (AP sites) to produce new 5'-ends that are base-free deoxyribose 5-phosphate residues. It preferentially attacks modified AP sites created by bleomycin and neocarzinostatin.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qu/1qum_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=1qum ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1QUM 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 ZN as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Deoxyribonuclease_IV_(phage-T(4)-induced) Deoxyribonuclease IV (phage-T(4)-induced)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.2 3.1.21.2] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1QUM OCA].
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*[[Endonuclease 3D structures|Endonuclease 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Structure of the DNA repair enzyme endonuclease IV and its DNA complex: double-nucleotide flipping at abasic sites and three-metal-ion catalysis., Hosfield DJ, Guan Y, Haas BJ, Cunningham RP, Tainer JA, Cell. 1999 Aug 6;98(3):397-408. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10458614 10458614]
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[[Category: Deoxyribonuclease IV (phage-T(4)-induced)]]
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[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Cunningham, R.P.]]
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[[Category: Cunningham RP]]
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[[Category: Guan, Y.]]
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[[Category: Guan Y]]
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[[Category: Haas, B.J.]]
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[[Category: Haas BJ]]
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[[Category: Hosfield, D.J.]]
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[[Category: Hosfield DJ]]
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[[Category: Tainer, J.A.]]
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[[Category: Tainer JA]]
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[[Category: ZN]]
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[[Category: dna repair enzyme]]
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[[Category: enzyme:dna complex]]
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[[Category: tim barrel]]
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[[Category: trinuclear zn cluster]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 01:00:13 2007''
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Current revision

CRYSTAL STRUCTURE OF ESCHERICHIA COLI ENDONUCLEASE IV IN COMPLEX WITH DAMAGED DNA

PDB ID 1qum

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