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2kzz

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[[Image:2kzz.gif|left|200px]]<br />
 
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<applet load="2kzz" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2kzz, resolution 2.25&Aring;" />
 
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'''KLENOW FRAGMENT WITH NORMAL SUBSTRATE AND ZINC ONLY'''<br />
 
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==Overview==
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==KLENOW FRAGMENT WITH NORMAL SUBSTRATE AND ZINC ONLY==
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The interaction of a divalent metal ion with a leaving 3' oxygen is a, central component of several proposed mechanisms of phosphoryl transfer., In support of this are recent kinetic studies showing that thiophilic, metal ions (e.g., Mn2+) stimulate the hydrolysis of compounds in which, sulfur takes the place of the leaving oxygen. To examine the structural, basis of this phenomenon, we have solved four crystal structures of, single-stranded DNA's containing either oxygen or sulfur at a 3'-bridging, position bound in conjunction with various metal ions at the 3'-5', exonucleolytic active site of the Klenow fragment (KF) of DNA polymerase I, from Escherichia coli. Two structures of normal ssDNA bound to KF in the, presence of Zn2+ and Mn2+ or Zn2+ alone were refined at 2.6- and 2.25-A, resolution, respectively. They serve as standards for comparison with, other Mn2+- and Zn2+-containing structures. In these cases, Mn2+ and Zn2+, bind at metal ion site B in a nearly identical position to Mg2+ (Brautigam, and Steitz (1998) J. Mol. Biol. 277, 363-377). Two structures of KF bound, to a deoxyoligonucleotide that contained a 3'-bridging sulfur at the, scissile phosphate were refined at 2.03-A resolution. Although the, bridging sulfur compounds bind in a manner very similar to that of the, normal oligonucleotides, the presence of the sulfur changes the metal ion, binding properties of the active site such that Mn2+ and Zn2+ are observed, at metal ion site B, but Mg2+ is not. It therefore appears that the, ability of the bridging sulfur compounds to exclude nonthiophilic metal, ions from metal ion site B explains the low activity of KF exonuclease on, these substrates in the presence of Mg2+ (Curley et al. (1997) J. Am., Chem. Soc. 119, 12691-12692) and that the 3'-bridging atom of the, substrate is influencing the binding of metal ion B prior to catalysis.
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<StructureSection load='2kzz' size='340' side='right'caption='[[2kzz]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2kzz]] 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=2KZZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KZZ 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]] 2.25&#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=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=2kzz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kzz OCA], [https://pdbe.org/2kzz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2kzz RCSB], [https://www.ebi.ac.uk/pdbsum/2kzz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2kzz ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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.
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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/kz/2kzz_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=2kzz 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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2KZZ 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/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] Structure known Active Site: EXO. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2KZZ OCA].
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*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Structures of normal single-stranded DNA and deoxyribo-3'-S-phosphorothiolates bound to the 3'-5' exonucleolytic active site of DNA polymerase I from Escherichia coli., Brautigam CA, Sun S, Piccirilli JA, Steitz TA, Biochemistry. 1999 Jan 12;38(2):696-704. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9888810 9888810]
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[[Category: DNA-directed DNA polymerase]]
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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: Brautigam, C.A.]]
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[[Category: Brautigam CA]]
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[[Category: Piccirilli, J.A.]]
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[[Category: Piccirilli JA]]
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[[Category: Steitz, T.A.]]
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[[Category: Steitz TA]]
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[[Category: Sun, S.]]
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[[Category: Sun S]]
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[[Category: ZN]]
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[[Category: exonuclease]]
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[[Category: nucleotidyltransferase/dna complex]]
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[[Category: polymerase]]
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[[Category: two metal ion]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 5 18:36:36 2007''
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Current revision

KLENOW FRAGMENT WITH NORMAL SUBSTRATE AND ZINC ONLY

PDB ID 2kzz

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