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001-es BibID:	BIBFORM031412
035-os BibID:	PMID:18020376 WOS:000251547700018
Első szerző:	Mones, Letif
Cím:	Probing the two-metal ion mechanism in the restriction endonuclease BamHI / Letif Mones, Petr Kulhánek, Jan Florián, István Simon, Monika Fuxreiter
Dátum:	2007
ISSN:	0006-2960
Megjegyzések:	The choreography of restriction endonuclease catalysis is a long-standing paradigm in molecular biology. Bivalent metal ions are required almost for all PD..D/ExK type enzymes, but the number of cofactors essential for the DNA backbone scission remained ambiguous. On the basis of crystal structures and biochemical data for various restriction enzymes, three models have been developed that assign critical roles for one, two, or three metal ions during the phosphodiester hydrolysis. To resolve this apparent controversy, we investigated the mechanism of BamHI catalysis using quantum mechanical/molecular mechanical simulation techniques and determined the activation barriers of three possible pathways that involve a Glu-113 or a neighboring water molecule as a general base or an external nucleophile that penetrated from bulk solution. The extrinsic mechanism was found to be the most favorable with an activation free energy of 23.4 kcal/mol, in reasonable agreement with the experimental data. On the basis of the effect of the individual metal ions on the activation barrier, metal ion A was concluded to be pivotal for the reaction, while the enzyme lacking metal ion B still has moderate efficiency. Thus, we propose that the catalytic scheme of BamHI does not involve a general base for nucleophile generation and requires one obligatory metal ion for catalysis that stabilizes the attacking nucleophile and coordinates it throughout the nucleophilic attack. Such a model may also explain the variation in the number of metal ions in the crystal structures and thus could serve as a framework for a unified catalytic scheme of type II restriction endonucleases.
Tárgyszavak:	Természettudományok Biológiai tudományok idegen nyelvű folyóiratközlemény külföldi lapban külföldön készült közlemény
Megjelenés:	Biochemistry. - 46 : 50 (2007), p. 14514-14523. -
További szerzők:	Kulhánek, Petr Florián, Jan Simon István Fuxreiter Mónika (1969-) (kutató vegyész)
Pályázati támogatás:	T049073 OTKA F046164 OTKA
Internet cím:	Intézményi repozitóriumban (DEA) tárolt változat DOI
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