1rzt

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(New page: 200px<br /> <applet load="1rzt" size="450" color="white" frame="true" align="right" spinBox="true" caption="1rzt, resolution 2.10&Aring;" /> '''Crystal structure o...)
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[[Image:1rzt.gif|left|200px]]<br />
 
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<applet load="1rzt" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1rzt, resolution 2.10&Aring;" />
 
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'''Crystal structure of DNA polymerase lambda complexed with a two nucleotide gap DNA molecule'''<br />
 
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==Overview==
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==Crystal structure of DNA polymerase lambda complexed with a two nucleotide gap DNA molecule==
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Human DNA polymerase lambda (Pol lambda) is a family X member with low, frameshift fidelity that has been suggested to perform gap-filling DNA, synthesis during base excision repair and during repair of broken ends, with limited homology. Here, we present a 2.1 A crystal structure of the, catalytic core of Pol lambda in complex with DNA containing a two, nucleotide gap. Pol lambda makes limited contacts with the template strand, at the polymerase active site, and superimposition with Pol beta in a, ternary complex suggests a shift in the position of the DNA at the active, site that is reminiscent of a deletion intermediate. Surprisingly, Pol, lambda can adopt a closed conformation, even in the absence of dNTP, binding. These observations have implications for the catalytic mechanism, and putative DNA repair functions of Pol lambda.
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<StructureSection load='1rzt' size='340' side='right'caption='[[1rzt]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1rzt]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RZT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RZT 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]] 2.1&#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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=1rzt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rzt OCA], [https://pdbe.org/1rzt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rzt RCSB], [https://www.ebi.ac.uk/pdbsum/1rzt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rzt ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DPOLL_HUMAN DPOLL_HUMAN] Repair polymerase. Involved in base excision repair (BER) responsible for repair of lesions that give rise to abasic (AP) sites in DNA. Has both DNA polymerase and terminal transferase activities. Has a 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity.<ref>PMID:11457865</ref> <ref>PMID:15537631</ref>
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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/rz/1rzt_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1rzt ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Human DNA polymerase lambda (Pol lambda) is a family X member with low frameshift fidelity that has been suggested to perform gap-filling DNA synthesis during base excision repair and during repair of broken ends with limited homology. Here, we present a 2.1 A crystal structure of the catalytic core of Pol lambda in complex with DNA containing a two nucleotide gap. Pol lambda makes limited contacts with the template strand at the polymerase active site, and superimposition with Pol beta in a ternary complex suggests a shift in the position of the DNA at the active site that is reminiscent of a deletion intermediate. Surprisingly, Pol lambda can adopt a closed conformation, even in the absence of dNTP binding. These observations have implications for the catalytic mechanism and putative DNA repair functions of Pol lambda.
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==About this Structure==
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A structural solution for the DNA polymerase lambda-dependent repair of DNA gaps with minimal homology.,Garcia-Diaz M, Bebenek K, Krahn JM, Blanco L, Kunkel TA, Pedersen LC Mol Cell. 2004 Feb 27;13(4):561-72. PMID:14992725<ref>PMID:14992725</ref>
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1RZT is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with NA and EDO as [http://en.wikipedia.org/wiki/ligands ligands]. 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=1RZT OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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A structural solution for the DNA polymerase lambda-dependent repair of DNA gaps with minimal homology., Garcia-Diaz M, Bebenek K, Krahn JM, Blanco L, Kunkel TA, Pedersen LC, Mol Cell. 2004 Feb 27;13(4):561-72. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=14992725 14992725]
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</div>
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[[Category: DNA-directed DNA polymerase]]
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<div class="pdbe-citations 1rzt" style="background-color:#fffaf0;"></div>
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[[Category: Homo sapiens]]
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[[Category: Single protein]]
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[[Category: Bebenek, K.]]
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[[Category: Blanco, L.]]
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[[Category: Garcia-Diaz, M.]]
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[[Category: Krahn, J.M.]]
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[[Category: Kunkel, T.A.]]
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[[Category: Pedersen, L.C.]]
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[[Category: EDO]]
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[[Category: NA]]
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[[Category: dna polymerase lambda]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 19:08:53 2007''
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==See Also==
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*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Homo sapiens]]
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[[Category: Large Structures]]
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[[Category: Bebenek K]]
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[[Category: Blanco L]]
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[[Category: Garcia-Diaz M]]
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[[Category: Krahn JM]]
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[[Category: Kunkel TA]]
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[[Category: Pedersen LC]]

Current revision

Crystal structure of DNA polymerase lambda complexed with a two nucleotide gap DNA molecule

PDB ID 1rzt

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