1bpe: Difference between revisions

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-[[Image:1bpe.gif|left|200px]]
- {{Structure
+==CRYSTAL STRUCTURE OF RAT DNA POLYMERASE BETA; EVIDENCE FOR A COMMON POLYMERASE MECHANISM==
-|PDB= 1bpe |SIZE=350|CAPTION= <scene name='initialview01'>1bpe</scene>, resolution 2.9&Aring;
+<StructureSection load='1bpe' size='340' side='right'caption='[[1bpe]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=DTP:2&#39;-DEOXYADENOSINE+5&#39;-TRIPHOSPHATE'>DTP</scene>
+<table><tr><td colspan='2'>[[1bpe]] is a 1 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=1BPE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BPE FirstGlance]. <br>
-|ACTIVITY= <span class='plainlinks'>[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] </span>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1bpe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bpe OCA], [https://pdbe.org/1bpe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bpe RCSB], [https://www.ebi.ac.uk/pdbsum/1bpe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bpe ProSAT]</span></td></tr>
-|RELATEDENTRY=
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1bpe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bpe OCA], [http://www.ebi.ac.uk/pdbsum/1bpe PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1bpe RCSB]</span>
+== Function ==
-}}
+[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.
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bp/1bpe_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=1bpe ConSurf].
+<div style="clear:both"></div>
-'''CRYSTAL STRUCTURE OF RAT DNA POLYMERASE BETA; EVIDENCE FOR A COMMON POLYMERASE MECHANISM'''
+==See Also==
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-Structures of the 31-kilodalton catalytic domain of rat DNA polymerase beta (pol beta) and the whole 39-kilodalton enzyme were determined at 2.3 and 3.6 angstrom resolution, respectively. The 31-kilodalton domain is composed of fingers, palm, and thumb subdomains arranged to form a DNA binding channel reminiscent of the polymerase domains of the Klenow fragment of Escherichia coli DNA polymerase I, HIV-1 reverse transcriptase, and bacteriophage T7 RNA polymerase. The amino-terminal 8-kilodalton domain is attached to the fingers subdomain by a flexible hinge. The two invariant aspartates found in all polymerase sequences and implicated in catalytic activity have the same geometric arrangement within structurally similar but topologically distinct palms, indicating that the polymerases have maintained, or possibly re-evolved, a common nucleotidyl transfer mechanism. The location of Mn2+ and deoxyadenosine triphosphate in pol beta confirms the role of the invariant aspartates in metal ion and deoxynucleoside triphosphate binding.
+[[Category: Large Structures]]
-==About this Structure==
-BPE is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BPE OCA].
-==Reference==
-Crystal structure of rat DNA polymerase beta: evidence for a common polymerase mechanism., Sawaya MR, Pelletier H, Kumar A, Wilson SH, Kraut J, Science. 1994 Jun 24;264(5167):1930-5. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/7516581 7516581]
-[[Category: DNA-directed DNA polymerase]]
 [[Category: Rattus norvegicus]]
-[[Category: Single protein]]
+[[Category: Kraut J]]
-[[Category: Kraut, J.]]
+[[Category: Kumar A]]
-[[Category: Kumar, A.]]
+[[Category: Pelletier H]]
-[[Category: Pelletier, H.]]
+[[Category: Sawaya MR]]
-[[Category: Sawaya, M R.]]
+[[Category: Wilson SH]]
-[[Category: Wilson, S H.]]
-[[Category: nucleotidyltransferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:05:40 2008''