2bpc: Difference between revisions

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New page: left|200px<br /><applet load="2bpc" size="450" color="white" frame="true" align="right" spinBox="true" caption="2bpc, resolution 2.80Å" /> '''CRYSTAL STRUCTURE OF...
 
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[[Image:2bpc.jpg|left|200px]]<br /><applet load="2bpc" size="450" color="white" frame="true" align="right" spinBox="true"
caption="2bpc, resolution 2.80&Aring;" />
'''CRYSTAL STRUCTURE OF RAT DNA POLYMERASE BETA: EVIDENCE FOR A COMMON POLYMERASE MECHANISM'''<br />


==Overview==
==CRYSTAL STRUCTURE OF RAT DNA POLYMERASE BETA: EVIDENCE FOR A COMMON POLYMERASE MECHANISM==
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.
<StructureSection load='2bpc' size='340' side='right'caption='[[2bpc]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2bpc]] 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=2BPC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BPC FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2bpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bpc OCA], [https://pdbe.org/2bpc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bpc RCSB], [https://www.ebi.ac.uk/pdbsum/2bpc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bpc ProSAT]</span></td></tr>
</table>
== 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/2bpc_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=2bpc ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
2BPC 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 MN 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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2BPC OCA].
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
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://ispc.weizmann.ac.il//pmbin/getpm?pmid=7516581 7516581]
[[Category: Large Structures]]
[[Category: DNA-directed DNA polymerase]]
[[Category: Rattus norvegicus]]
[[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: MN]]
[[Category: nucleotidyltransferase]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 08:52:00 2007''

Latest revision as of 12:17, 14 February 2024

CRYSTAL STRUCTURE OF RAT DNA POLYMERASE BETA: EVIDENCE FOR A COMMON POLYMERASE MECHANISMCRYSTAL STRUCTURE OF RAT DNA POLYMERASE BETA: EVIDENCE FOR A COMMON POLYMERASE MECHANISM

Structural highlights

2bpc is a 1 chain structure with sequence from Rattus norvegicus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.8Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

2bpc, resolution 2.80Å

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