Chemistry Reference
In-Depth Information
cofactor: high level of similarity of the active site with other viral integrases;
J. Mol. Biol.
,
1998 ,
282
, 359 - 368 .
Bujacz , G. ; Jaskolski , M. ; Alexandratos , J. ; Wlodawer , A. ; Merkel , G. ; Katz , R.A.
et al.
;
High-resolution structure of the catalytic domain of avian sarcoma virus integrase;
J. Mol. Biol.
, 1995 ,
253
, 333 - 346 .
Sapienza , P.J. ; Rosenberg , J.M. ; Jen - Jacobson , L. ; Structural and thermodynamic basis
for enhanced DNA binding by a promiscuous mutant EcoRI endonuclease;
Structure
,
2007 ,
15
, 1368 - 1382 .
Horton , N.C. ; Perona , J.J.; DNA cleavage by EcoRV endonuclease: two metal ions in
three metal ion binding sites;
Biochem.
, 2004 ,
43
, 6841 - 6857 .
Galburt , E.A. ; Stoddard , B.L. ; Catalytic mechanisms of restriction and homing endonu-
cleases ;
Biochem.
, 2002 ,
41
, 13851 - 13860 .
Kim , Y.C. ; Grable , J.C. ; Love , R. ; Greene , P.J. ; Rosenberg , J.M. ; Refi nement of
Eco
RI
endonuclease crystal structure: a revised protein chain tracing;
Science
, 1990 ,
249
,
1307 - 1309 .
Horton , J.R. ; Cheng , X. ;
Pvu
II endonuclease contains two calcium ions in active sites;
J. Mol. Biol.
, 2000 ,
300
, 1049 - 1056 .
Nowotny , M. ; Gaidamakov , S.A. ; Ghirlando , R. ; Cerritelli , S.M. ; Crouch , R.J. ; Yang , W. ;
Structure of human RNase H1 complexed with an RNA/DNA hybrid: insight into HIV
reverse transcription;
Mol. Cell
, 2007 ,
28
, 264 - 276 .
Viadiu , H. ; Aggarwal , A.K. ; Structure of BamHI bound to nonspecifi c DNA: a model
for DNA sliding;
Mol. Cell
, 2000 ,
5
, 889 - 895 .
Bowen , L.M. ; Muller , G. ; Riehl , J.P. ; Dupureur , C.M. ; Lanthanide spectroscopic studies
of the dinuclear and Mg(II)-dependent PvuII restriction endonuclease;
Biochem.
, 2004 ,
43
, 15286 - 15295 .
Xu , Q.S. ; Kucera , R.B. ; Roberts , R.J. ; Guo , H.C. ; An asymmetric complex of restriction
endonuclease MspI on its palindromic DNA recognition site;
Structure
, 2004 ,
12
,
1741 - 1747 .
Vipond , I.B. ; Halford , S.E. ; Specifi c DNA recognition by EcoRV restriction endonucle-
ase induced by calcium ions;
Biochem.
, 1995 ,
34
, 1113 - 1119 .
Kim , E.E. ; Wyckoff , H.W. ; Reaction mechanism of alkaline phosphatase based on crystal
structures. Two - metal ion catalysis ;
J. Mol. Biol.
, 1992 ,
218
, 449 - 464 .
Beese , L.S. ; Steitz , T.A.; Structural basis for the 3′ - 5 ′ exonuclease activity of
Escherichia
coli
DNA polymerase I: a two metal ion mechanism;
EMBO J.
, 1992 ,
10
, 25 - 33 .
Steitz , T.A. ; Steitz , J.A. ; A general two - metal - ion mechanism for catalytic RNA ;
Proc.
Natl. Acad. Sci. USA
, 1993 ,
90
, 6498 - 6502 .
Tolia , N.H. ; Joshua - Tor , L. ; Slicer and the argonautes;
Nat. Chem. Biol.
, 2007 ,
3
,
36 - 43 .
Nowotny , M. ; Yang , W.; Stepwise analyses of metal ions in RNase H catalysis from sub-
strate destabilization to product release;
EMBO J.
, 2006 ,
25
, 1924 - 1933 .
Pauling , L. ; Atomic radii and interatomic distances in metals ;
J. Am. Chem. Soc.
, 1947 ,
69
, 542 - 553 .
Kunkel , T.A. ; Tcheng , J.E. ; Meyer , R.R. ; Purifi cation and properties of DNA polymerase-
beta from guinea pig liver;
Biochim. Biophys. Acta
, 1978 ,
520
, 302 - 316 .
Ling , H. ; Boudsocq , F. ; Plosky , B.S. ; Woodgate , R. ; Yang , W. ; Replication of a cis - syn
thymine dimer at atomic resolution;
Nature
, 2003 ,
424
, 1083 - 1087 .
Vipond , I.B. ; Baldwin , G.S. ; Halford , S.E. ; Divalent metal ions at the active sites of the
EcoRV and EcoRI restriction endonucleases;
Biochem.
, 1995 ,
34
, 697 - 704 .
Viadiu , H. ; Aggarwal , A.K.; The role of metals in catalysis by the restriction endonucle-
ase BamHI;
Nat. Struct. Biol.
, 1998 ,
5
, 910 - 916 .
Ling , H. ; Boudsocq , F. ; Woodgate , R. ; Yang , W. ; Snapshots of replication through an
abasic lesion; structural basis for base substitutions and frameshifts;
Mol. Cell
, 2004 ,
13
,
751 - 762 .
Weis , W.I. ; Drickamer , K. ; Hendrickson , W.A. ; Structure of a C - type mannose - binding
protein complexed with an oligosaccharide;
Nature
, 1992 ,
360
, 127 - 134 .
71.
72.
73.
74.
75.
76.
77.
78.
79.
80.
81.
82.
83.
84.
85.
86.
87.
88.
89.
90.
91.
92.
93.
