4nlg: Difference between revisions
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==Y-family DNA polymerase chimera Dbh-Dpo4(243-245)-Dbh== | |||
<StructureSection load='4nlg' size='340' side='right' caption='[[4nlg]], [[Resolution|resolution]] 2.40Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4nlg]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_33909 Atcc 33909]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NLG OCA]. <br> | |||
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene><br> | |||
<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dbh, Saci_0554 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2285 ATCC 33909])</td></tr> | |||
<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></td></tr> | |||
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4nlg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nlg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nlg RCSB], [http://www.ebi.ac.uk/pdbsum/4nlg PDBsum]</span></td></tr> | |||
<table> | |||
<div style="background-color:#fffaf0;"> | |||
== 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®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
== References == | |||
== | <references/> | ||
__TOC__ | |||
</StructureSection> | |||
[[Category: Atcc 33909]] | |||
[[Category: DNA-directed DNA polymerase]] | [[Category: DNA-directed DNA polymerase]] | ||
[[Category: Mukherjee, P.]] | [[Category: Mukherjee, P.]] | ||