Metal-binding sites at the active site of restriction endonuclease BamHI can conform to a one-ion mechanism

被引：11

作者：

Mones, Letif ^{[1
]}

Simon, Istvan ^{[1
]}

Fuxreiter, Monika ^{[1
]}

机构：

[1] Hungarian Acad Sci, Biol Res Ctr, Inst Enzymol, H-1113 Budapest, Hungary

来源：

BIOLOGICAL CHEMISTRY | 2007年 / 388卷 / 01期

基金：

匈牙利科学研究基金会;

关键词：

metal ion cofactors; phosphoryl transfer; restriction endonucleases; two-metal ion mechanism;

D O I：

10.1515/BC.2007.009

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The number of metal ions required for phosphoryl transfer in restriction endonucleases is still an unresolved question in molecular biology. The two Ca2+ and Mn2+ ions observed in the pre- and post-reactive complexes of BamHI conform to the classical two-metal ion choreography. We probed the Mg2+ cofactor positions at the active site of BamHI by molecular dynamics simulations with one and two metal ions present and identified several catalytically relevant sites. These can mark the pathway of a single ion during catalysis, suggesting its critical role, while a regulatory function is proposed for a possible second ion.

引用

页码：73 / 78

页数：6

共 40 条

[21] SUBSTRATE-ASSISTED CATALYSIS IN THE CLEAVAGE OF DNA BY THE ECORI AND ECORV RESTRICTION ENZYMES [J].

JELTSCH, A ;

ALVES, J ;

WOLFES, H ;

MAASS, G ;

PINGOUD, A .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1993, 90 (18) :8499-8503

[22] COMPARISON OF SIMPLE POTENTIAL FUNCTIONS FOR SIMULATING LIQUID WATER [J].

JORGENSEN, WL ;

CHANDRASEKHAR, J ;

MADURA, JD ;

IMPEY, RW ;

KLEIN, ML .

JOURNAL OF CHEMICAL PHYSICS, 1983, 79 (02) :926-935

[23] Structural, functional, and evolutionary relationships between λ-exonuclease and the type II restriction endonucleases [J].

Kovall, RA ;

Matthews, BW .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1998, 95 (14) :7893-7897

[24] MutH complexed with hemi- and unmethylated DNAs: Coupling base recognition and DNA cleavage [J].

Lee, JY ;

Chang, J ;

Joseph, N ;

Ghirlando, R ;

Rao, DN ;

Yang, W .

MOLECULAR CELL, 2005, 20 (01) :155-166

[25] Two-metal active site binding of a Tn5 transposase synaptic complex [J].

Lovell, S ;

Goryshin, IY ;

Reznikoff, WR ;

Rayment, I .

NATURE STRUCTURAL BIOLOGY, 2002, 9 (04) :278-281

[26]

Lukacs CM, 2000, NAT STRUCT BIOL, V7, P134

[27] Q:: A molecular dynamics program for free energy calculations and empirical valence bond simulations in biomolecular systems [J].

Marelius, J ;

Kolmodin, K ;

Feierberg, I ;

Åqvist, J .

JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 1998, 16 (4-6) :213-+

[28] Crystal structure of restriction endonuclease Bg/I bound to its interrupted DNA recognition sequence [J].

Newman, M ;

Lunnen, K ;

Wilson, G ;

Greci, J ;

Schildkraut, I ;

Phillips, SEV .

EMBO JOURNAL, 1998, 17 (18) :5466-5476

[29] The role of GyrB in the DNA cleavage-religation reaction of DNA gyrase: A proposed two metal-ion mechanism [J].

Noble, CG ;

Maxwell, A .

JOURNAL OF MOLECULAR BIOLOGY, 2002, 318 (02) :361-371

[30] Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release [J].

Nowotny, Marcin ;

Yang, Wei .

EMBO JOURNAL, 2006, 25 (09) :1924-1933

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