4ebe | pdb_00004ebe
Conformationally Restrained North-methanocarba-2'-deoxyadenosine Corrects the Error-Prone Nature of Human DNA Polymerase Iota
Structural highlights
Function[POLI_HUMAN] Error-prone DNA polymerase specifically involved in DNA repair. Plays an important role in translesion synthesis, where the normal high-fidelity DNA polymerases cannot proceed and DNA synthesis stalls. Favors Hoogsteen base-pairing in the active site. Inserts the correct base with high-fidelity opposite an adenosine template. Exhibits low fidelity and efficiency opposite a thymidine template, where it will preferentially insert guanosine. May play a role in hypermutation of immunogobulin genes. Forms a Schiff base with 5'-deoxyribose phosphate at abasic sites, but may not have lyase activity.[1] [2] [3] [4] [5] [6] [7] Publication Abstract from PubMedY-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 iota) is the most error-prone. In the current study, we elucidate the molecular basis for improving the fidelity of hpol iota through use of the fixed-conformation nucleotide North-methanocarba-2'-deoxyadenosine triphosphate (N-MC-dATP). Three crystal structures were solved of hpol iota in complex with DNA containing a template 2'-deoxythymidine (dT) paired with an incoming dNTP or modified nucleotide triphosphate. The ternary complex of hpol iota inserting N-MC-dATP opposite dT reveals that the adenine ring is stabilized in the anti orientation about the pseudo-glycosyl torsion angle (chi), which mimics precisely the mutagenic arrangement of dGTP:dT normally preferred by hpol iota. 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 iota by preventing the Hoog-steen base-pairing mode normally observed for hpol iota-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. A nucleotide analogue induced gain of function corrects the error-prone nature of human DNA polymerase iota.,Ketkar A, Zafar MK, Banerjee S, Marquez VE, Egli M, Eoff RL J Am Chem Soc. 2012 May 26. PMID:22632140[8] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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