|
|
| (2 intermediate revisions by the same user not shown) |
| Line 1: |
Line 1: |
|
| |
|
| ==Crystal structure of Dpo4 in complex with N-MC-dAMP opposite dT== | | ==Crystal structure of Dpo4 in complex with N-MC-dAMP opposite dT== |
| <StructureSection load='4gc6' size='340' side='right' caption='[[4gc6]], [[Resolution|resolution]] 2.90Å' scene=''> | | <StructureSection load='4gc6' size='340' side='right'caption='[[4gc6]], [[Resolution|resolution]] 2.90Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
| <table><tr><td colspan='2'>[[4gc6]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulso Sulso]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GC6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GC6 FirstGlance]. <br> | | <table><tr><td colspan='2'>[[4gc6]] 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=4GC6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GC6 FirstGlance]. <br> |
| </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0OH:NORTH-METHANOCARBA-2-DEOXYADENOSINE+TRIPHOSPHATE'>0OH</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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]] 2.895Å</td></tr> |
| <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2agq|2agq]], [[3pr5|3pr5]], [[2j6s|2j6s]], [[3t5j|3t5j]], [[4gc7|4gc7]]</td></tr>
| | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0OH:NORTH-METHANOCARBA-2-DEOXYADENOSINE+TRIPHOSPHATE'>0OH</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr> |
| <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dbh, dpo4, SSO2448 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273057 SULSO])</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=4gc6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gc6 OCA], [https://pdbe.org/4gc6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gc6 RCSB], [https://www.ebi.ac.uk/pdbsum/4gc6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gc6 ProSAT]</span></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=4gc6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gc6 OCA], [http://pdbe.org/4gc6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4gc6 RCSB], [http://www.ebi.ac.uk/pdbsum/4gc6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4gc6 ProSAT]</span></td></tr> | |
| </table> | | </table> |
| == Function == | | == Function == |
| [[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] | | [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. |
| <div style="background-color:#fffaf0;">
| |
| == Publication Abstract from PubMed ==
| |
| DNA polymerases select for the incorporation of deoxyribonucleotide triphosphates (dNTPs) using amino acid side-chains that act as a "steric-gate" to bar improper incorporation of rNTPs. An additional factor in the selection of nucleotide substrates resides in the preferred geometry for the furanose moiety of the incoming nucleotide triphosphate. We have probed the role of sugar geometry during nucleotide selection by model DNA polymerases from Sulfolobus solfataricus using fixed conformation nucleotide analogues. North-methanocarba-dATP (N-MC-dATP) locks the central ring into a RNA-type (C2'-exo, North) conformation near a C3'-endo pucker and South-methanocarba-dATP (S-MC-dATP) locks the central ring system into a (C3'-exo, South) conformation near a C2'-endo pucker. Dpo4 preferentially inserts N-MC-dATP and in the crystal structure of Dpo4 in complex with N-MC-dAMP, the nucleotide analogue superimposes almost perfectly with Dpo4 bound to unmodified dATP. Biochemical assays indicate that the S. solfataricus B-family DNA polymerase Dpo1 can insert and extend from both N-MC-dATP and S-MC-dATP. In this respect, Dpo1 is unexpectedly more tolerant of substrate conformation than Dpo4. The crystal structure of Dpo4 bound to S-MC-dADP shows that poor incorporation of the Southern pucker by the Y-family polymerase results from a hydrogen bond between the 3 -OH group of the nucleotide analogue and the OH group of the steric gate residue, Tyr12, shifting the S-MC-dADP molecule away from the dNTP binding pocket and distorting the bp at the primer-template junction. These results provide insights into substrate specificity of DNA polymerases, as well as molecular mechanisms that act as a barrier against insertion of rNTPs.
| |
| | |
| Differential furanose selection in the active sites of archaeal DNA polymerases probed by fixed-conformation nucleotide analogues.,Ketkar A, Zafar MK, Marquez VE, Banerjee S, Egli M, Eoff RL Biochemistry. 2012 Oct 11. PMID:23050956<ref>PMID:23050956</ref>
| |
| | |
| From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| |
| </div>
| |
| <div class="pdbe-citations 4gc6" style="background-color:#fffaf0;"></div>
| |
|
| |
|
| ==See Also== | | ==See Also== |
| *[[DNA polymerase|DNA polymerase]] | | *[[DNA polymerase 3D structures|DNA polymerase 3D structures]] |
| == References ==
| |
| <references/>
| |
| __TOC__ | | __TOC__ |
| </StructureSection> | | </StructureSection> |
| [[Category: DNA-directed DNA polymerase]] | | [[Category: Large Structures]] |
| [[Category: Sulso]] | | [[Category: Saccharolobus solfataricus P2]] |
| [[Category: Banerjee, S]] | | [[Category: Banerjee S]] |
| [[Category: Eoff, R L]] | | [[Category: Eoff RL]] |
| [[Category: Ketkar, A]] | | [[Category: Ketkar A]] |
| [[Category: Zafar, M K]] | | [[Category: Zafar MK]] |
| [[Category: Dna polymerase]]
| |
| [[Category: Transferase-dna complex]]
| |