Metal-ion dependence of the active-site conformation of the translesion DNA polymerase Dpo4 from Sulfolobus solfataricus.
Crystal structures of a binary Mg2+-form Dpo4-DNA complex with 1,N2-etheno-dG in the template strand as well as of ternary Mg2+-form Dpo4-DNA-dCTP/dGTP complexes with 8-oxoG in the template strand have been determined. Comparison of their conformations and active-site geometries with those of the corresponding Ca2+-form complexes revealed that the DNA and polymerase undergo subtle changes as a result of the catalytically more active Mg2+ occupying both the A and B sites.
Irimia
Adriana
A
Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University, Nashville, TN 37232, USA.
Loukachevitch
Lioudmila V
LV
Eoff
Robert L
RL
Guengerich
F Peter
FP
Egli
Martin
M
D055162:Biocatalysis; D002118:Calcium / Q000737:chemistry* / Q000378:metabolism; D020134:Catalytic Domain; D002413:Cations, Divalent / Q000737:chemistry / Q000378:metabolism; D018360:Crystallography, X-Ray; D019951:DNA Polymerase beta / Q000737:chemistry*; D008274:Magnesium / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D011485:Protein Binding; D040681:Structural Homology, Protein; D048229:Sulfolobus solfataricus / Q000201:enzymology*
D002413:Cations, Divalent; D019951:DNA Polymerase beta; D008274:Magnesium; D002118:Calcium
Proc Natl Acad Sci U S A. 2007 Oct 2;104(40):15591-8
17898175
PLoS Biol. 2006 Jan;4(1):e11
16379496
J Biol Chem. 2007 Dec 14;282(50):36421-33
17951245
Cell. 2001 Oct 5;107(1):91-102
11595188
Biochemistry. 2009 Aug 4;48(30):7079-88
19492857
Chem Rev. 2006 Feb;106(2):420-52
16464013
J Biol Chem. 2005 Aug 19;280(33):29750-64
15965231
Nat Struct Mol Biol. 2004 May;11(5):457-62
15077104
J Biol Chem. 2009 Feb 6;284(6):3563-76
19059910
Annu Rev Biochem. 2005;74:317-53
15952890
J Appl Crystallogr. 2007 Aug 1;40(Pt 4):658-674
19461840
Mol Cell. 2004 Mar 12;13(5):751-62
15023344
Nature. 2003 Aug 28;424(6952):1083-7
12904819
J Biol Chem. 2006 Jan 27;281(4):2358-72
16306039
J Biol Chem. 2007 May 4;282(18):13573-84
17337730
Nat Struct Mol Biol. 2010 Mar;17(3):379-88
20154704
Acta Crystallogr D Biol Crystallogr. 1998 Sep 1;54(Pt 5):905-21
9757107
Methods Enzymol. 1997;276:307-26
27754618
Biochemistry. 2004 Feb 24;43(7):2116-25
14967051
Biochemistry. 2008 Jul 15;47(28):7322-34
18563918
J Biol Chem. 2007 Jan 12;282(2):1456-67
17105728
J Biol Chem. 2009 Jun 26;284(26):17687-99
19542237
Nucleic Acids Res. 2001 Nov 15;29(22):4607-16
11713310
J Biol Chem. 2009 Aug 14;284(33):22467-22480
19542228
EMBO J. 2005 Sep 7;24(17):2957-67
16107880
Biochemistry. 2006 May 16;45(19):5949-56
16681366
J Biol Chem. 2007 Jul 6;282(27):19831-43
17468100
Proc Natl Acad Sci U S A. 2004 Feb 24;101(8):2265-9
14982998