View source for 4nlg


==Y-family DNA polymerase chimera Dbh-Dpo4(243-245)-Dbh==
<StructureSection load='4nlg' size='340' side='right'caption='[[4nlg]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[4nlg]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Sulfolobus_acidocaldarius Sulfolobus acidocaldarius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NLG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NLG FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
<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=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene></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=4nlg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nlg OCA], [https://pdbe.org/4nlg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nlg RCSB], [https://www.ebi.ac.uk/pdbsum/4nlg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nlg ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DPO4_SULAC DPO4_SULAC] 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 (By similarity).
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== Publication Abstract from PubMed ==
Dpo4 and Dbh are from two closely related Sulfolobus species and are well-studied archaeal homologs of Pol IV, an error prone Y-family polymerase from E. coli. Despite sharing 54% amino acid identity, these polymerases display distinct mutagenic and translesion specificities. Structurally, Dpo4 and Dbh adopt different conformations owing to the difference in relative orientation of their N-terminal catalytic and C-terminal DNA binding domains. Using chimeric constructs of these two polymerases, we have previously demonstrated that the interdomain linker is a major determinant of polymerase conformation, base substitution fidelity and abasic site translesion synthesis. Here we find that the interdomain linker also affects the single-base deletion frequency and the mispair extension efficiency of these polymerases. Exchanging just three amino acids in the linkers of Dbh and Dpo4 is sufficient to change the fidelity by up to 30-fold, predominantly by altering the rate of correct (but not incorrect) nucleotide incorporation. Additionally, from a 2.4 A resolution crystal structure, we have found that the three linker amino acids from Dpo4 are sufficient to allow Dbh to adopt the standard conformation of Dpo4. Thus, a small region of the interdomain linker, located more than 11 A away from the catalytic residues, determines the fidelity of these Y-family polymerases, by controlling the alignment of substrates at the active site.

Three Residues of the Interdomain Linker Determine the Conformation and Single-Base Deletion Fidelity of Y-family Translesion Polymerases.,Mukherjee P, Wilson RC, Lahiri I, Pata JD J Biol Chem. 2014 Jan 10. PMID:24415763<ref>PMID:24415763</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 4nlg" style="background-color:#fffaf0;"></div>

==See Also==
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
== References ==
<references/>
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</StructureSection>
[[Category: Large Structures]]
[[Category: Sulfolobus acidocaldarius]]
[[Category: Mukherjee P]]
[[Category: Pata JD]]
[[Category: Wilson RC]]