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| | ==Structure of MsDpo4== | | ==Structure of MsDpo4== |
| - | <StructureSection load='4dez' size='340' side='right' caption='[[4dez]], [[Resolution|resolution]] 2.60Å' scene=''> | + | <StructureSection load='4dez' size='340' side='right'caption='[[4dez]], [[Resolution|resolution]] 2.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4dez]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_smegmatis Mycobacterium smegmatis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DEZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DEZ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4dez]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis_MC2_155 Mycolicibacterium smegmatis MC2 155]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DEZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DEZ FirstGlance]. <br> |
| - | </td></tr><tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dinB, dinB1, MSMEG_1014, MSMEG_2294 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1772 Mycobacterium smegmatis])</td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6Å</td></tr> |
| - | <tr><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'>[https://proteopedia.org/fgij/fg.htm?mol=4dez FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dez OCA], [https://pdbe.org/4dez PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dez RCSB], [https://www.ebi.ac.uk/pdbsum/4dez PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dez ProSAT]</span></td></tr> |
| - | <tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4dez FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dez OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dez RCSB], [http://www.ebi.ac.uk/pdbsum/4dez PDBsum]</span></td></tr> | + | </table> |
| - | <table> | + | == Function == |
| - | <div style="background-color:#fffaf0;">
| + | [https://www.uniprot.org/uniprot/A0QR77_MYCS2 A0QR77_MYCS2] 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, in conjunction with the beta clamp from PolIII (By similarity).[HAMAP-Rule:MF_01113] |
| - | == Publication Abstract from PubMed == | + | |
| - | Y-family DNA polymerases (dPols) have evolved to carry out translesion bypass to rescue stalled replication; prokaryotic members of this family also participate in the phenomenon of adaptive mutagenesis to relieve selection pressure imposed by a maladapted environment. In this study, the first structure of a member of this family from a prokaryote has been determined. The structure of MsPolIV, a Y-family dPol from Mycobacterium smegmatis, shows the presence of the characteristic finger, palm and thumb domains. Surprisingly, the electron-density map of the intact protein does not show density for the PAD region that is unique to members of this family. Analysis of the packing of the molecules in the crystals showed the existence of large solvent-filled voids in which the PAD region could be located in multiple conformations. In line with this observation, analytical gel-filtration and dynamic light-scattering studies showed that MsPolIV undergoes significant compaction upon DNA binding. The PAD region is known to insert into the major groove of the substrate DNA and to play a major role in shaping the active site. Comparison with structures of other Y-family dPols shows that in the absence of tertiary contacts between the PAD domain and the other domains this region has the freedom to adopt multiple orientations. This structural attribute of the PAD will allow these enzymes to accommodate the alterations in the width of the DNA double helix that are necessary to achieve translesion bypass and adaptive mutagenesis and will also allow regulation of their activity to prevent adventitious error-prone DNA synthesis.
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| - | The PAD region in the mycobacterial DinB homologue MsPolIV exhibits positional heterogeneity.,Sharma A, Subramanian V, Nair DT Acta Crystallogr D Biol Crystallogr. 2012 Aug;68(Pt 8):960-7. Epub 2012 Jul 17. PMID:22868761<ref>PMID:22868761</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| | ==See Also== | | ==See Also== |
| - | *[[DNA polymerase|DNA polymerase]] | + | *[[DNA polymerase 3D structures|DNA polymerase 3D structures]] |
| - | == References ==
| + | |
| - | <references/>
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: DNA-directed DNA polymerase]] | + | [[Category: Large Structures]] |
| - | [[Category: Mycobacterium smegmatis]] | + | [[Category: Mycolicibacterium smegmatis MC2 155]] |
| - | [[Category: Nair, D T.]] | + | [[Category: Nair DT]] |
| - | [[Category: Sharma, A.]] | + | [[Category: Sharma A]] |
| - | [[Category: Dna polymerase]]
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| - | [[Category: Transferase]]
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| - | [[Category: Y-family]]
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