2bpg

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(New page: 200px<br /><applet load="2bpg" size="450" color="white" frame="true" align="right" spinBox="true" caption="2bpg, resolution 3.600&Aring;" /> '''STRUCTURES OF TERNA...)
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[[Image:2bpg.jpg|left|200px]]<br /><applet load="2bpg" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2bpg, resolution 3.600&Aring;" />
 
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'''STRUCTURES OF TERNARY COMPLEXES OF RAT DNA POLYMERASE BETA, A DNA TEMPLATE-PRIMER, AND DDCTP'''<br />
 
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==Overview==
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==STRUCTURES OF TERNARY COMPLEXES OF RAT DNA POLYMERASE BETA, A DNA TEMPLATE-PRIMER, AND DDCTP==
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Two ternary complexes of rat DNA polymerase beta (pol beta), a DNA, template-primer, and dideoxycytidine triphosphate (ddCTP) have been, determined at 2.9 A and 3.6 A resolution, respectively. ddCTP is the, triphosphate of dideoxycytidine (ddC), a nucleoside analog that targets, the reverse transcriptase of human immunodeficiency virus (HIV) and is at, present used to treat AIDS. Although crystals of the two complexes belong, to different space groups, the structures are similar, suggesting that the, polymerase-DNA-ddCTP interactions are not affected by crystal packing, forces. In the pol beta active site, the attacking 3'-OH of the elongating, primer, the ddCTP phosphates, and two Mg2+ ions are all clustered around, Asp190, Asp192, and Asp256. Two of these residues, Asp190 and Asp256, are, present in the amino acid sequences of all polymerases so far studied and, are also spatially similar in the four polymerases--the Klenow fragment of, Escherichia coli DNA polymerase I, HIV-1 reverse transcriptase, T7 RNA, polymerase, and rat DNA pol beta--whose crystal structures are now known., A two-metal ion mechanism is described for the nucleotidyl transfer, reaction and may apply to all polymerases. In the ternary complex, structures analyzed, pol beta binds to the DNA template-primer in a, different manner from that recently proposed for other polymerase-DNA, models.
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<StructureSection load='2bpg' size='340' side='right'caption='[[2bpg]], [[Resolution|resolution]] 3.60&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2bpg]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BPG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BPG 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]] 3.6&#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=DCT:2,3-DIDEOXYCYTIDINE+5-TRIPHOSPHATE'>DCT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=2bpg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bpg OCA], [https://pdbe.org/2bpg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bpg RCSB], [https://www.ebi.ac.uk/pdbsum/2bpg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bpg ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DPOLB_RAT DPOLB_RAT] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.
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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/bp/2bpg_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=2bpg 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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2BPG is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus] with MG and DCT as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2BPG 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 ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP., Pelletier H, Sawaya MR, Kumar A, Wilson SH, Kraut J, Science. 1994 Jun 24;264(5167):1891-903. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7516580 7516580]
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[[Category: Large Structures]]
[[Category: Rattus norvegicus]]
[[Category: Rattus norvegicus]]
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[[Category: Single protein]]
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[[Category: Kraut J]]
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[[Category: Kraut, J.]]
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[[Category: Kumar A]]
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[[Category: Kumar, A.]]
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[[Category: Pelletier H]]
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[[Category: Pelletier, H.]]
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[[Category: Sawaya MR]]
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[[Category: Sawaya, M.R.]]
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[[Category: Wilson SH]]
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[[Category: Wilson, S.H.]]
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[[Category: DCT]]
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[[Category: MG]]
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[[Category: protein-dna complex]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 08:52:10 2007''
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STRUCTURES OF TERNARY COMPLEXES OF RAT DNA POLYMERASE BETA, A DNA TEMPLATE-PRIMER, AND DDCTP

PDB ID 2bpg

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