4EBC

Conformationally Restrained North-methanocarba-2'-deoxyadenosine Corrects the Error-Prone Nature of Human DNA Polymerase Iota

Summary for 4EBC

• Entry DOI: 10.2210/pdb4ebc/pdb
• Related: 1T3N 2ALZ 3GV5 3GV7 3GV8 3H40 4EBD 4EBE
• Descriptor: DNA polymerase iota, 5'-D(P*AP*GP*GP*AP*CP*CP*(DOC))-3', 5'-D(P*CP*TP*GP*GP*GP*TP*CP*CP*T)-3', ... (7 entities in total)
• Functional Keywords: polymerase, transferase-dna complex, transferase/dna
• Biological source: Homo sapiens (human)
• Cellular location: Nucleus: Q9UNA4
• Total number of polymer chains: 3
• Total formula weight: 52555.09

Authors

Eoff, R.L.,Ketkar, A.,Banerjee, S. (deposition date: 2012-03-23, release date: 2012-06-13, Last modification date: 2023-09-13)

Primary citation

Ketkar, A.,Zafar, M.K.,Banerjee, S.,Marquez, V.E.,Egli, M.,Eoff, R.L.
A Nucleotide-Analogue-Induced Gain of Function Corrects the Error-Prone Nature of Human DNA Polymerase iota.
J.Am.Chem.Soc., 134:10698-10705, 2012

PubMed Abstract: Y-family DNA polymerases participate in replication stress and DNA damage tolerance mechanisms. The properties that allow these enzymes to copy past bulky adducts or distorted template DNA can result in a greater propensity for them to make mistakes. Of the four human Y-family members, human DNA polymerase iota (hpol ι) is the most error-prone. In the current study, we elucidate the molecular basis for improving the fidelity of hpol ι through use of the fixed-conformation nucleotide North-methanocarba-2'-deoxyadenosine triphosphate (N-MC-dATP). Three crystal structures were solved of hpol ι in complex with DNA containing a template 2'-deoxythymidine (dT) paired with an incoming dNTP or modified nucleotide triphosphate. The ternary complex of hpol ι inserting N-MC-dATP opposite dT reveals that the adenine ring is stabilized in the anti orientation about the pseudo-glycosyl torsion angle, which mimics precisely the mutagenic arrangement of dGTP:dT normally preferred by hpol ι. The stabilized anti conformation occurs without notable contacts from the protein but likely results from constraints imposed by the bicyclo[3.1.0]hexane scaffold of the modified nucleotide. Unmodified dATP and South-MC-dATP each adopt syn glycosyl orientations to form Hoogsteen base pairs with dT. The Hoogsteen orientation exhibits weaker base-stacking interactions and is less catalytically favorable than anti N-MC-dATP. Thus, N-MC-dATP corrects the error-prone nature of hpol ι by preventing the Hoogsteen base-pairing mode normally observed for hpol ι-catalyzed insertion of dATP opposite dT. These results provide a previously unrecognized means of altering the efficiency and the fidelity of a human translesion DNA polymerase.

PubMed: 22632140
DOI: 10.1021/ja304176q

Experimental method

X-RAY DIFFRACTION (2.901 Å)