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1im4

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(New page: 200px<br /><applet load="1im4" size="450" color="white" frame="true" align="right" spinBox="true" caption="1im4, resolution 2.30&Aring;" /> '''Crystal Structure of...)
Current revision (07:36, 7 February 2024) (edit) (undo)
 
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[[Image:1im4.jpg|left|200px]]<br /><applet load="1im4" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1im4, resolution 2.30&Aring;" />
 
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'''Crystal Structure of a DinB Homolog (DBH) Lesion Bypass DNA Polymerase Catalytic Fragment from Sulfolobus solfataricus'''<br />
 
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==Overview==
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==Crystal Structure of a DinB Homolog (DBH) Lesion Bypass DNA Polymerase Catalytic Fragment from Sulfolobus solfataricus==
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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.
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<StructureSection load='1im4' size='340' side='right'caption='[[1im4]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1im4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus Saccharolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IM4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IM4 FirstGlance]. <br>
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1IM4 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus] with SO4 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=1IM4 OCA].
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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]] 2.3&#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=SO4:SULFATE+ION'>SO4</scene></td></tr>
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==Reference==
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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=1im4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1im4 OCA], [https://pdbe.org/1im4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1im4 RCSB], [https://www.ebi.ac.uk/pdbsum/1im4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1im4 ProSAT]</span></td></tr>
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11545744 11545744]
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</table>
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[[Category: DNA-directed DNA polymerase]]
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== Function ==
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[[Category: Single protein]]
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[https://www.uniprot.org/uniprot/DPO4_SACSO DPO4_SACSO] 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.
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[[Category: Sulfolobus solfataricus]]
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== Evolutionary Conservation ==
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[[Category: Pata, J.D.]]
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[[Image:Consurf_key_small.gif|200px|right]]
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[[Category: Steitz, T.A.]]
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Check<jmol>
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[[Category: Zhou, B.L.]]
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<jmolCheckbox>
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[[Category: SO4]]
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/im/1im4_consurf.spt"</scriptWhenChecked>
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[[Category: dna polymerase palm]]
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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[[Category: fidelity]]
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<text>to colour the structure by Evolutionary Conservation</text>
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[[Category: fingers]]
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</jmolCheckbox>
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[[Category: helix-hairpin-helix]]
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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=1im4 ConSurf].
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[[Category: processivity]]
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<div style="clear:both"></div>
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[[Category: thumb]]
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__TOC__
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</StructureSection>
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 17:29:59 2007''
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[[Category: Large Structures]]
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[[Category: Saccharolobus solfataricus]]
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[[Category: Pata JD]]
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[[Category: Steitz TA]]
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[[Category: Zhou BL]]

Current revision

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

PDB ID 1im4

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