4qwd

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==TERNARY CRYSTAL STRUCTURES of A Y-FAMILY DNA POLYMERASE DPO4 FROM SULFOLOBUS SOLFATARICUS IN COMPLEX WITH DNA AND (-)3TC-PPNP==
==TERNARY CRYSTAL STRUCTURES of A Y-FAMILY DNA POLYMERASE DPO4 FROM SULFOLOBUS SOLFATARICUS IN COMPLEX WITH DNA AND (-)3TC-PPNP==
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<StructureSection load='4qwd' size='340' side='right' caption='[[4qwd]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
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<StructureSection load='4qwd' size='340' side='right'caption='[[4qwd]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4qwd]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QWD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QWD FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4qwd]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus_P2 Saccharolobus solfataricus P2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QWD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QWD FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3TT:[[[[(2R,5S)-5-(4-AZANYL-2-OXIDANYLIDENE-PYRIMIDIN-1-YL)-1,3-OXATHIOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL]OXY-OXIDANYL-PHOSPHORYL]AMINO]PHOSPHONIC+ACID'>3TT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 2.05&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4qw8|4qw8]], [[4qw9|4qw9]], [[4qwa|4qwa]], [[4qwb|4qwb]], [[4qwc|4qwc]], [[4qwe|4qwe]]</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=3TT:[[[[(2R,5S)-5-(4-AZANYL-2-OXIDANYLIDENE-PYRIMIDIN-1-YL)-1,3-OXATHIOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL]OXY-OXIDANYL-PHOSPHORYL]AMINO]PHOSPHONIC+ACID'>3TT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</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=4qwd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qwd OCA], [https://pdbe.org/4qwd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qwd RCSB], [https://www.ebi.ac.uk/pdbsum/4qwd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qwd 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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4qwd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qwd OCA], [http://pdbe.org/4qwd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qwd RCSB], [http://www.ebi.ac.uk/pdbsum/4qwd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4qwd ProSAT]</span></td></tr>
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</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/DPO4_SULSO DPO4_SULSO]] 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. It is involved in translesional synthesis.[HAMAP-Rule:MF_01113]
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[https://www.uniprot.org/uniprot/DPO4_SACS2 DPO4_SACS2] 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. It is involved in translesional synthesis.
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Considering that all natural nucleotides (D-dNTPs) and the building blocks (D-dNMPs) of DNA chains possess D-stereochemistry, DNA polymerases and reverse transcriptases (RTs) likely possess strongD-stereoselectivity by preferably binding and incorporating D-dNTPs over unnatural L-dNTPs during DNA synthesis. Surprisingly, a structural basis for the discrimination against L-dNTPs by DNA polymerases or RTs has not been established although L-deoxycytidine analogs (lamivudine and emtricitabine) and L-thymidine (telbivudine) have been widely used as antiviral drugs for years. Here we report seven high-resolution ternary crystal structures of a prototype Y-family DNA polymerase, DNA, and D-dCTP, D-dCDP, L-dCDP, or the diphosphates and triphosphates of lamivudine and emtricitabine. These structures reveal that relative to D-dCTP, each of these L-nucleotides has its sugar ring rotated by 180 degrees with an unusual O4'-endo sugar puckering and exhibits multiple triphosphate-binding conformations within the active site of the polymerase. Such rare binding modes significantly decrease the incorporation rates and efficiencies of these L-nucleotides catalyzed by the polymerase.
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Structural and kinetic insights into binding and incorporation of L-nucleotide analogs by a Y-family DNA polymerase.,Gaur V, Vyas R, Fowler JD, Efthimiopoulos G, Feng JY, Suo Z Nucleic Acids Res. 2014 Aug 7. pii: gku709. PMID:25104018<ref>PMID:25104018</ref>
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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 4qwd" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
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*[[DNA polymerase|DNA polymerase]]
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*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: DNA-directed DNA polymerase]]
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[[Category: Large Structures]]
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[[Category: Gaur, V]]
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[[Category: Saccharolobus solfataricus P2]]
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[[Category: Suo, Z]]
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[[Category: Gaur V]]
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[[Category: Transferase-dna complex]]
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[[Category: Suo Z]]
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[[Category: Y-family dna polymerase]]
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Current revision

TERNARY CRYSTAL STRUCTURES of A Y-FAMILY DNA POLYMERASE DPO4 FROM SULFOLOBUS SOLFATARICUS IN COMPLEX WITH DNA AND (-)3TC-PPNP

PDB ID 4qwd

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