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6vdd

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Current revision (14:37, 6 March 2024) (edit) (undo)
 
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<StructureSection load='6vdd' size='340' side='right'caption='[[6vdd]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
<StructureSection load='6vdd' size='340' side='right'caption='[[6vdd]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6vdd]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_smegmatis"_trevisan_1889 "bacillus smegmatis" trevisan 1889]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VDD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VDD FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6vdd]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis Mycolicibacterium smegmatis] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VDD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VDD FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DCT:2,3-DIDEOXYCYTIDINE+5-TRIPHOSPHATE'>DCT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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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]] 1.9&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">polA, MSMEI_3749 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1772 "Bacillus smegmatis" Trevisan 1889])</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=DCT:2,3-DIDEOXYCYTIDINE+5-TRIPHOSPHATE'>DCT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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<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>
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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=6vdd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vdd OCA], [https://pdbe.org/6vdd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vdd RCSB], [https://www.ebi.ac.uk/pdbsum/6vdd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vdd ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6vdd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vdd OCA], [http://pdbe.org/6vdd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vdd RCSB], [http://www.ebi.ac.uk/pdbsum/6vdd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vdd ProSAT]</span></td></tr>
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</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/I7G3P9_MYCS2 I7G3P9_MYCS2]] In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity.[RuleBase:RU004460]
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[https://www.uniprot.org/uniprot/A0QYZ2_MYCS2 A0QYZ2_MYCS2] In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity.[RuleBase:RU004460]
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Mycobacterial Pol1 is a bifunctional enzyme composed of an N-terminal DNA flap endonuclease/5' exonuclease domain (FEN/EXO) and a C-terminal DNA polymerase domain (POL). Here we document additional functions of Pol1: FEN activity on the flap RNA strand of an RNA:DNA hybrid and reverse transcriptase activity on a DNA-primed RNA template. We report crystal structures of the POL domain, as apoenzyme and as ternary complex with 3'-dideoxy-terminated DNA primer-template and dNTP. The thumb, palm, and fingers subdomains of POL form an extensive interface with the primer-template and the triphosphate of the incoming dNTP. Progression from an open conformation of the apoenzyme to a nearly closed conformation of the ternary complex entails a disordered-to-ordered transition of several segments of the thumb and fingers modules and an inward motion of the fingers subdomain-especially the O helix-to engage the primer-template and dNTP triphosphate. Distinctive structural features of mycobacterial Pol1 POL include a manganese binding site in the vestigial 3' exonuclease subdomain and a non-catalytic water-bridged magnesium complex at the protein-DNA interface. We report a crystal structure of the bifunctional FEN/EXO-POL apoenzyme that reveals the positions of two active site metals in the FEN/EXO domain.
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Mycobacterial DNA polymerase I: activities and crystal structures of the POL domain as apoenzyme and in complex with a DNA primer-template and of the full-length FEN/EXO-POL enzyme.,Ghosh S, Goldgur Y, Shuman S Nucleic Acids Res. 2020 Feb 8. pii: 5730378. doi: 10.1093/nar/gkaa075. PMID:32034423<ref>PMID:32034423</ref>
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==See Also==
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*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 6vdd" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Bacillus smegmatis trevisan 1889]]
 
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[[Category: DNA-directed DNA polymerase]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Ghosh, S]]
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[[Category: Mycolicibacterium smegmatis]]
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[[Category: Goldgur, Y]]
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[[Category: Synthetic construct]]
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[[Category: Shuman, S]]
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[[Category: Ghosh S]]
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[[Category: Apoenzyme]]
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[[Category: Goldgur Y]]
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[[Category: Dna polymerase]]
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[[Category: Shuman S]]
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[[Category: Mycobacteria]]
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[[Category: Transferase-dna complex]]
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Current revision

POL domain of Pol1 from M. smegmatis complex with DNA primer-template and dNTP

PDB ID 6vdd

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