1im4

From Proteopedia

(Difference between revisions)

Revision as of 09:11, 10 January 2018

Crystal Structure of a DinB Homolog (DBH) Lesion Bypass DNA Polymerase Catalytic Fragment from Sulfolobus solfataricus

Structural highlights

1im4 is a 1 chain structure with sequence from Atcc 35091. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:	DBH (ATCC 35091)
Activity:	DNA-directed DNA polymerase, with EC number 2.7.7.7
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[DPO4_SULSF] Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. May be involved in translesional synthesis.

Evolutionary Conservation

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

Publication Abstract from PubMed

The UmuC/DinB family of bypass polymerases is responsible for translesion DNA synthesis and includes the human polymerases eta, iota, and kappa. We determined the 2.3 A resolution crystal structure of a catalytic fragment of the DinB homolog (Dbh) polymerase from Sulfolobus solfataricus and show that it is nonprocessive and can bypass an abasic site. The structure of the catalytic domain is nearly identical to those of most other polymerase families. Homology modeling suggests that there is minimal contact between protein and DNA, that the nascent base pair binding pocket is quite accessible, and that the enzyme is already in a closed conformation characteristic of ternary polymerase complexes. These observations afford insights into the sources of low fidelity and low processivity of the UmuC/DinB polymerases.

Crystal structure of a DinB lesion bypass DNA polymerase catalytic fragment reveals a classic polymerase catalytic domain.,Zhou BL, Pata JD, Steitz TA Mol Cell. 2001 Aug;8(2):427-37. PMID:11545744^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Zhou BL, Pata JD, Steitz TA. Crystal structure of a DinB lesion bypass DNA polymerase catalytic fragment reveals a classic polymerase catalytic domain. Mol Cell. 2001 Aug;8(2):427-37. PMID:11545744

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1im4"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of a DinB Homolog (DBH) Lesion Bypass DNA Polymerase Catalytic Fragment from Sulfolobus solfataricus==
 <StructureSection load='1im4' size='340' side='right' caption='[[1im4]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
@@ Line 6: / Line 7: @@
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DBH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 ATCC 35091])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1im4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1im4 OCA], [http://pdbe.org/1im4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1im4 RCSB], [http://www.ebi.ac.uk/pdbsum/1im4 PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1im4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1im4 OCA], [http://pdbe.org/1im4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1im4 RCSB], [http://www.ebi.ac.uk/pdbsum/1im4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1im4 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 14: / Line 15: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/im/1im4_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/im/1im4_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>

1im4

From Proteopedia

Revision as of 09:11, 10 January 2018

Crystal Structure of a DinB Homolog (DBH) Lesion Bypass DNA Polymerase Catalytic Fragment from Sulfolobus solfataricus

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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