Chemistry Reference
In-Depth Information
51.
Garcia - Diaz , M. ; Bebenek , K. ; Krahn , J.M. ; Pedersen , L.C.
; Kunkel , T.A.; Role of the
catalytic metal during polymerization by DNA polymerase lambda;
DNA Repair
(Amst.)
,
2007 ,
6
, 1333 - 1340 .
Garcia - Diaz , M. ; Bebenek , K. ; Krahn , J.M. ; Kunkel , T.A. ; Pedersen , L.C. ; A closed con-
formation for the Pol lambda catalytic cycle;
Nat. Struct. Mol. Biol.
, 2005 ,
12
, 97 - 98 .
Showalter , A.K. ; Tsai , M.D. ; A reexamination of the nucleotide incorporation fi delity of
DNA polymerases;
Biochem.
, 2002 ,
41
, 10571 - 10576 .
Wong , I. ; Patel , S.S. ; Johnson , K.A. ; An induced - fi t kinetic mechanism for DNA replica-
tion fi delity: direct measurement by single- turnover
52.
53.
54.
kinetics ;
Biochem.
,
1992 ,
30
,
526 - 537 .
Li , Y. ; Korolev , S. ; Waksman , G. ; Crystal structures of open and closed forms of binary
and ternary complexes of the large fragment of
Thermus aquaticus
DNA polymerase I:
structural basis for nucleotide incorporation;
EMBO J.
, 1998 ,
17
, 7514 - 7525 .
Shah , A.M. ; Li , S.X. ; Anderson , K.S. ; Sweasy , J.B.; Y265H mutator mutant of DNA
polymerase beta. Proper teometric alignment is critical for fi delity;
J. Biol. Chem.
, 2001 ,
276
, 10824 - 10831 .
Zhong , X. ; Patel , S.S. ; Werneburg , B.G. ; Tsai , M.D. ; DNA polymerase beta: multiple
conformational changes in the mechanism of catalysis;
Biochem.
,
55.
56.
57.
1997 ,
36
,
11891 - 11900 .
Bakhtina , M. ; Lee , S. ; Wang , Y. ; Dunlap , C. ; Lamarche , B. ; Tsai , M.D. ; Use of viscogens,
dNTPalphaS, and rhodium(III) as probes in stopped- fl ow experiments to obtain new
evidence for the mechanism of catalysis by DNA polymerase beta;
Biochem.
, 2005 ,
44
,
5177 - 5187 .
Rothwell , P.J. ; Mitaksov , V. ; Waksman , G. ; Motions of the fi ngers subdomain of klentaq1
are fast and not rate limiting: implications for the molecular basis of fi delity in DNA
polymerases ;
Mol. Cell
, 2005 ,
19
, 345 - 355 .
Zhang , H. ; Cao , W. ; Zakharova , E. ; Konigsberg , W. ; De La Cruz , E.M. ; Fluorescence of
2-aminopurine reveals rapid conformational changes in the RB69 DNA polymerase-
primer/template complexes upon binding and incorporation of matched deoxynucleo-
side triphosphates;
Nucleic Acids Res.
, 2007 ,
35
, 6052 - 6062 .
Fiala , K.A.; Suo, Z.; Mechanism of DNA polymerization catalyzed by Sulfolobus solfa-
taricus P2 DNA polymerase IV;
Biochem.
, 2004 ,
43
, 2116 - 2125 .
Song , J.J. ; Smith , S.K. ; Hannon , G.J. ; Joshua - Tor , L. ; Crystal structure of Argonaute and
its implications for RISC slicer activity;
Science
, 2004 ,
305
, 1434 - 1437 .
Nowotny , M. ; Gaidamakov , S.A. ; Crouch , R.J. ; Yang , W. ; Crystal structures of RNase H
bound to an RNA/DNA hybrid: substrate specifi city and metal- dependent catalysis ;
Cell
,
2005 ,
121
, 1005 - 1016 .
Steiniger - White , M. ; Rayment , I. ; Reznikoff , W.S. ; Structure/function insights into Tn5
transposition ;
Curr. Opin. Struct. Biol.
, 2004 ,
14
, 50 - 57 .
Pingoud , A. ; Fuxreiter , M. ; Pingoud , V. ; Wende , W. ; Type II restriction endonucleases:
structure and mechanism;
Cell Mol. Life Sci.
, 2005 ,
62
, 685 - 707 .
Kovall , R.A. ; Matthews , B.W.; Structural, functional, and evolutionary relationships
between lambda-exonuclease and the type II restriction endonucleases;
Proc. Natl. Acad.
Sci. USA
, 1998 ,
95
, 7893 - 7897 .
Lee , J.Y. ; Chang , J. ; Joseph , N. ; Ghirlando , R. ; Rao , D.N. ; Yang , W. ; MutH complexed with
hemi- and unmethylated DNAs: coupling base recognition and DNA cleavage;
Mol. Cell
,
2005 ,
20
, 155 - 166 .
Goedken , E.R. ; Marqusee , S. ; Co - crystal of
Escherichia coli
RNase HI with Mn2+ ions
reveals two divalent metals bound in the active site;
J. Biol. Chem.
,
58.
59.
60.
61.
62.
63.
64.
65.
66.
67.
68.
2001 ,
276
,
7266 - 7271 .
Tsunaka , Y. ; Takano , K. ; Matsumura , H. ; Yamagata , Y. ; Kanaya , S. ; Identifi cation of single
Mn(2+) binding sites required for activation of the mutant proteins of E.coli RNase HI
at Glu48 and/or Asp134 by X- ray crystallography ;
J. Mol. Biol.
, 2005 ,
345
, 1171 - 1183 .
Maignan , S. ; Guilloteau , J.P. ;
69.
70.
Zhou - Liu , Q. ; Clement - Mella , C. ; Mikol , V. ; Crystal struc-
tures of the catalytic domain of HIV-1 integrase free and complexed with its metal