8ick | pdb_00008ick

DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DATP (1 MILLIMOLAR), MGCL2 (5 MILLIMOLAR), AND MNCL2 (5 MILLIMOLAR)

spinqualitylabelsall models 8ick, resolution 2.70Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 8ick is a 3 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: DTP, MN, NA Related: 7ice, 7icf, 7icg, 7ich, 7ici, 7icj, 7ick, 7icl, 7icm, 7icn, 7ico, 7icp, 7icq, 7icr, 7ics, 7ict, 7icu, 7icv, 8ica, 8icb, 8icc, 8ice, 8icf, 8icg, 8ich, 8ici, 8icj, 8icl, 8icm, 8icn, 8ico, 8icp, 8icq, 8icr, 8ics, 8ict, 8icu, 8icv, 8icw, 8icx, 8icy, 8icz, 9ica, 9icb, 9icc, 9ice, 9icf, 9icg, 9ich, 9ici, 9icj, 9ick, 9icl, 9icm, 9icn, 9ico, 9icp, 9icq, 9icr, 9ics, 9ict, 9icu, 9icv, 9icw, 9icx, 9icy, 1zqa, 1zqb, 1zqc, 1zqd, 1zqe, 1zqf, 1zqg, 1zqh, 1zqi, 1zqj, 1zqk, 1zql, 1zqm, 1zqn, 1zqo, 1zqp, 1zqq, 1zqr, 1zqs, 1zqt Resources: FirstGlance, OCA, RCSB, PDBsum Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMed When crystals of human DNA polymerase beta (pol beta) complexed with DNA [Pelletier, H., Sawaya, M. R., Wolfle, W., Wilson, S. H., & Kraut, J. (1996) Biochemistry 35, 12742-12761] are soaked in the presence of dATP and Mn2+, X-ray structural analysis shows that nucleotidyl transfer to the primer 3'-OH takes place directly in the crystals, even though the DNA is blunt-ended at the active site. Under similar crystal-soaking conditions, there is no evidence for a reaction when Mn2+ is replaced by Mg2+, which is thought to be the divalent metal ion utilized by most polymerases in vivo. These results suggest that one way Mn2+ may manifest its mutagenic effect on polymerases is by promoting greater reactivity than Mg2+ at the catalytic site, thereby allowing the nucleotidyl transfer reaction to take place with little or no regard to instructions from a template. Non-template-directed nucleotidyl transfer is also observed when pol beta-DNA cocrystals are soaked in the presence of dATP and Zn2+, but the reaction products differ in that the sugar moiety of the incorporated nucleotide appears distorted or otherwise cleaved, in agreement with reports that Zn2+ may act as a polymerase inhibitor rather than as a mutagen [Sirover, M. A., & Loeb, L. A. (1976) Science 194, 1434-1436]. Although no reaction is observed when crystals are soaked in the presence of dATP and other metal ions such as Ca2+, Co2+, Cr3+, or Ni2+, X-ray structural analyses show that these metal ions coordinate the triphosphate moiety of the nucleotide in a manner that differs from that observed with Mg2+. In addition, all metal ions tested, with the exception of Mg2+, promote a change in the side-chain position of aspartic acid 192, which is one of three highly conserved active-site carboxylate residues. Soaking experiments with nucleotides other than dATP (namely, dCTP, dGTP, dTTP, ATP, ddATP, ddCTP, AZT-TP, and dATP alpha S) reveal a non-base-specific binding site on pol beta for the triphosphate and sugar moieties of a nucleotide, suggesting a possible mechanism for nucleotide selectivity whereby triphosphate-sugar binding precedes a check for correct base pairing with the template. A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta.,Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J Biochemistry. 1996 Oct 1;35(39):12762-77. PMID:8841119 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also DNA polymerase

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