4ruc

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==Crystal structure of Y-family DNA polymerase Dpo4 extending from a MeFapy-dG:dC pair==
==Crystal structure of Y-family DNA polymerase Dpo4 extending from a MeFapy-dG:dC pair==
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<StructureSection load='4ruc' size='340' side='right' caption='[[4ruc]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
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<StructureSection load='4ruc' size='340' side='right'caption='[[4ruc]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4ruc]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RUC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RUC FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4ruc]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus_P2 Saccharolobus solfataricus P2] 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=4RUC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RUC 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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</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]] 2.9&#8491;</td></tr>
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<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MF7:N-{2-AMINO-5-[FORMYL(METHYL)AMINO]-6-HYDROXYPYRIMIDIN-4-YL}-2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYLAMINE'>MF7</scene></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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=MF7:N-{2-AMINO-5-[FORMYL(METHYL)AMINO]-6-HYDROXYPYRIMIDIN-4-YL}-2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYLAMINE'>MF7</scene></td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ru9|4ru9]], [[4rua|4rua]]</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=4ruc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ruc OCA], [https://pdbe.org/4ruc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ruc RCSB], [https://www.ebi.ac.uk/pdbsum/4ruc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ruc ProSAT]</span></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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ruc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ruc OCA], [http://pdbe.org/4ruc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ruc RCSB], [http://www.ebi.ac.uk/pdbsum/4ruc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ruc 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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N(6)-(2-Deoxy-d-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylf ormamidopyrimidine (MeFapy-dG) arises from N7-methylation of deoxyguanosine followed by imidazole ring opening. The lesion has been reported to persist in animal tissues. Previous in vitro replication bypass investigations of the MeFapy-dG adduct revealed predominant insertion of C opposite the lesion, dependent on the identity of the DNA polymerase (Pol) and the local sequence context. Here we report crystal structures of ternary Pol.DNA.dNTP complexes between MeFapy-dG-adducted DNA template:primer duplexes and the Y-family polymerases human Pol eta and P2 Pol IV (Dpo4) from Sulfolobus solfataricus. The structures of the hPol eta and Dpo4 complexes at the insertion and extension stages, respectively, are representative of error-free replication, with MeFapy-dG in the anti conformation and forming Watson-Crick pairs with dCTP or dC.
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Structural Basis for Error-Free Bypass of the 5-N-Methylformamidopyrimidine-dG Lesion by Human DNA Polymerase eta and Sulfolobus solfataricus P2 Polymerase IV.,Patra A, Banerjee S, Johnson Salyard TL, Malik CK, Christov PP, Rizzo CJ, Stone MP, Egli M J Am Chem Soc. 2015 Jun 10;137(22):7011-4. doi: 10.1021/jacs.5b02701. Epub 2015, May 27. PMID:25988947<ref>PMID:25988947</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 4ruc" 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: DNA-directed DNA polymerase]]
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[[Category: Large Structures]]
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[[Category: Banerjee, S]]
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[[Category: Saccharolobus solfataricus P2]]
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[[Category: Egli, M]]
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[[Category: Synthetic construct]]
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[[Category: Patra, A]]
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[[Category: Banerjee S]]
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[[Category: Stone, M P]]
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[[Category: Egli M]]
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[[Category: Adenosine triphosphate]]
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[[Category: Patra A]]
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[[Category: Dna]]
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[[Category: Stone MP]]
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[[Category: Dna binding]]
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[[Category: Dna damage]]
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[[Category: Dna-directed dna polymerase]]
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[[Category: Mefapy-dg lesion bypass]]
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[[Category: Primer extension]]
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[[Category: Protein]]
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[[Category: Transferase-dna complex]]
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[[Category: Y-family polymerase]]
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Current revision

Crystal structure of Y-family DNA polymerase Dpo4 extending from a MeFapy-dG:dC pair

PDB ID 4ruc

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