1waf: Difference between revisions

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New page: left|200px<br /><applet load="1waf" size="450" color="white" frame="true" align="right" spinBox="true" caption="1waf, resolution 3.2Å" /> '''DNA POLYMERASE FROM B...
 
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[[Image:1waf.gif|left|200px]]<br /><applet load="1waf" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1waf, resolution 3.2&Aring;" />
'''DNA POLYMERASE FROM BACTERIOPHAGE RB69'''<br />


==Overview==
==DNA POLYMERASE FROM BACTERIOPHAGE RB69==
The 2.8 A resolution crystal structure of the bacteriophage RB69 gp43, a, member of the eukaryotic pol alpha family of replicative DNA polymerases, shares some similarities with other polymerases but shows many, differences. Although its palm domain has the same topology as other, polymerases, except rat DNA polymerase beta, one of the three carboxylates, required for nucleotidyl transfer is located on a different beta strand., The structures of the fingers and thumb domains are unrelated to all other, known polymerase structures. The editing 3'-5' exonuclease domain of gp43, is homologous to that of E. coli DNA polymerase I but lies on the opposite, side of the polymerase active site. An extended structure-based alignment, of eukaryotic DNA polymerase sequences provides structural insights that, should be applicable to most eukaryotic DNA polymerases.
<StructureSection load='1waf' size='340' side='right'caption='[[1waf]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1waf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_phage_RB69 Escherichia phage RB69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WAF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WAF 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]] 3.2&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GMP:GUANOSINE'>GMP</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=1waf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1waf OCA], [https://pdbe.org/1waf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1waf RCSB], [https://www.ebi.ac.uk/pdbsum/1waf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1waf ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DPOL_BPR69 DPOL_BPR69] This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single stranded DNA in the 3'- to 5'-direction.
== 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/wa/1waf_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=1waf ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1WAF is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_rb18 Enterobacteria phage rb18] with GMP 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=1WAF OCA].
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Crystal structure of a pol alpha family replication DNA polymerase from bacteriophage RB69., Wang J, Sattar AK, Wang CC, Karam JD, Konigsberg WH, Steitz TA, Cell. 1997 Jun 27;89(7):1087-99. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9215631 9215631]
[[Category: Escherichia phage RB69]]
[[Category: DNA-directed DNA polymerase]]
[[Category: Large Structures]]
[[Category: Enterobacteria phage rb18]]
[[Category: Karam JD]]
[[Category: Single protein]]
[[Category: Konigsberg WH]]
[[Category: Karam, J.D.]]
[[Category: Satter AKMA]]
[[Category: Konigsberg, W.H.]]
[[Category: Steitz TA]]
[[Category: Satter, A.K.M.A.]]
[[Category: Wang CC]]
[[Category: Steitz, T.A.]]
[[Category: Wang J]]
[[Category: Wang, C.C.]]
[[Category: Wang, J.]]
[[Category: GMP]]
[[Category: nucleotidyltransferase]]
[[Category: rb69 dna polymerase (gp43)]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 05:16:46 2007''

Latest revision as of 11:47, 14 February 2024

DNA POLYMERASE FROM BACTERIOPHAGE RB69DNA POLYMERASE FROM BACTERIOPHAGE RB69

Structural highlights

1waf is a 2 chain structure with sequence from Escherichia phage RB69. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 3.2Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DPOL_BPR69 This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single stranded DNA in the 3'- to 5'-direction.

Evolutionary Conservation

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

See Also

1waf, resolution 3.20Å

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