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1d9d

From Proteopedia

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[[Image:1d9d.gif|left|200px]]
 
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{{Structure
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==CRYSTALL STRUCTURE OF THE COMPLEX OF DNA POLYMERASE I KLENOW FRAGMENT WITH SHORT DNA FRAGMENT CARRYING 2'-0-AMINOPROPYL-RNA MODIFICATIONS 5'-D(TCG)-AP(AUC)-3'==
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|PDB= 1d9d |SIZE=350|CAPTION= <scene name='initialview01'>1d9d</scene>, resolution 2.18&Aring;
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<StructureSection load='1d9d' size='340' side='right'caption='[[1d9d]], [[Resolution|resolution]] 2.18&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> and <scene name='pdbligand=SO4:SULFATE ION'>SO4</scene>
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<table><tr><td colspan='2'>[[1d9d]] 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=1D9D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D9D FirstGlance]. <br>
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|ACTIVITY= [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]
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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]] 2.18&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C31:2-O-3-AMINOPROPYL+CYTIDINE-5-MONOPHOSPHATE'>C31</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=U31:2-O-3-AMINOPROPYL+2-DEOXYURIDINE-5-MONOPHOSPHATE'>U31</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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}}
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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=1d9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d9d OCA], [https://pdbe.org/1d9d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d9d RCSB], [https://www.ebi.ac.uk/pdbsum/1d9d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d9d 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/d9/1d9d_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=1d9d ConSurf].
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<div style="clear:both"></div>
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'''CRYSTALL STRUCTURE OF THE COMPLEX OF DNA POLYMERASE I KLENOW FRAGMENT WITH SHORT DNA FRAGMENT CARRYING 2'-0-AMINOPROPYL-RNA MODIFICATIONS 5'-D(TCG)-AP(AUC)-3''''
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==See Also==
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*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
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__TOC__
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==Overview==
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</StructureSection>
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Nuclease resistance and RNA affinity are key criteria in the search for optimal antisense nucleic acid modifications, but the origins of the various levels of resistance to nuclease degradation conferred by chemical modification of DNA and RNA are currently not understood. The 2'-O-aminopropyl (AP)-RNA modification displays the highest nuclease resistance among all phosphodiester-based analogues and its RNA binding affinity surpasses that of phosphorothioate DNA by 1 degrees C per modified residue. We found that oligodeoxynucleotides containing AP-RNA residues at their 3' ends competitively inhibit the degradation of single-stranded DNA by the Escherichia coli Klenow fragment (KF) 3'-5' exonuclease and snake venom phosphodiesterase. To shed light on the origins of nuclease resistance brought about by the AP modification, we determined the crystal structure of an A-form DNA duplex with AP-RNA modifications at 1.6-A resolution. In addition, the crystal structures of complexes between short DNA fragments carrying AP-RNA modifications and wild-type KF were determined at resolutions between 2.2 and 3.0 A and compared with the structure of the complex between oligo(dT) and the D355A/E357A KF mutant. The structural models suggest that interference of the positively charged 2'-O-substituent with the metal ion binding site B of the exonuclease allows AP-RNA to effectively slow down degradation.
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==About this Structure==
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1D9D 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=1D9D OCA].
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==Reference==
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Structural origins of the exonuclease resistance of a zwitterionic RNA., Teplova M, Wallace ST, Tereshko V, Minasov G, Symons AM, Cook PD, Manoharan M, Egli M, Proc Natl Acad Sci U S A. 1999 Dec 7;96(25):14240-5. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10588690 10588690]
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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: Cook, P D.]]
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[[Category: Cook PD]]
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[[Category: Egli, M.]]
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[[Category: Egli M]]
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[[Category: Manoharan, M.]]
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[[Category: Manoharan M]]
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[[Category: Minasov, G.]]
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[[Category: Minasov G]]
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[[Category: Simons, A M.]]
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[[Category: Simons AM]]
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[[Category: Teplova, M.]]
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[[Category: Teplova M]]
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[[Category: Tereshko, V.]]
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[[Category: Tereshko V]]
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[[Category: Wallace, S T.]]
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[[Category: Wallace ST]]
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[[Category: MG]]
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[[Category: SO4]]
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[[Category: ZN]]
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[[Category: 2'-o-aminopropyl nucleotide]]
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[[Category: klenow fragment]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:34:52 2008''
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Current revision

CRYSTALL STRUCTURE OF THE COMPLEX OF DNA POLYMERASE I KLENOW FRAGMENT WITH SHORT DNA FRAGMENT CARRYING 2'-0-AMINOPROPYL-RNA MODIFICATIONS 5'-D(TCG)-AP(AUC)-3'

PDB ID 1d9d

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