Three Metal Ions Participate in the Reaction Catalyzed by T5 Flap Endonuclease

Abstract

Protein nucleases and RNA enzymes depend on divalent metal ions to catalyze the rapid hydrolysis of phosphate diester linkages of nucleic acids during DNA replication, DNA repair, RNA processing, and RNA degradation. These enzymes are widely proposed to catalyze phosphate diester hydrolysis using a "two-metal-ion mechanism." Yet, analyses of flap endonuclease (FEN) family members, which occur in all domains of life and act in DNA replication and repair, exemplify controversies regarding the classical two-metal-ion mechanism for phosphate diester hydrolysis. Whereas substrate-free structures of FENs identify two active site metal ions, their typical separation of >4 Å appears incompatible with this mechanism. To clarify the roles played by FEN metal ions, we report here a detailed evaluation of the magnesium ion response of T5FEN. Kinetic investigations reveal that overall the T5FEN-catalyzed reaction requires at least three magnesium ions, implying that an additional metal ion is bound. The presence of at least two ions bound with differing affinity is required to catalyze phosphate diester hydrolysis. Analysis of the inhibition of reactions by calcium ions is consistent with a requirement for two viable cofactors (Mg 2؉ or Mn 2؉). The apparent substrate association constant is maximized by binding two magnesium ions. This may reflect a metal-dependent unpairing of duplex substrate required to position the scissile phosphate in contact with metal ion(s). The combined results suggest that T5FEN primarily uses a two-metal-ion mechanism for chemical catalysis, but that its overall metallobiochemistry is more complex and requires three ions.Key cellular processes such as DNA replication, DNA repair, RNA processing, and RNA degradation require the rapid hydrolysis of the phosphate diester linkages of nucleic acids. The uncatalyzed hydrolysis of phosphate diesters under biological conditions is an extremely slow process with an estimated half-life of 30 million years at 25°C (1). Protein nucleases and RNA enzymes produce rate enhancements of 10 15 -10 17 to allow this reaction to proceed on a biologically useful time scale. Most enzymes catalyzing phosphate diester bond hydrolysis have a requirement for divalent metal ions. Based largely upon crystallographic observations, most metallonucleases are proposed to catalyze reactions using a two-metal-ion mechanism (Fig. 1a) analogous to that suggested for the phosphate monoesterase alkaline phosphatase (2, 3), although this view is not universally accepted. Three recent reviews present contrasting views on the roles of metal ions in protein nuclease and RNA enzyme reactions and illustrate this controversy (4 -6).One family of metallonucleases over which there has been considerable mechanistic debate are the flap endonucleases (FENs) 3 (7-12), which are present in all domains of life and play a key role in DNA replication and repair. Unlike most metallonucleases, which typically possess a cluster of three or four active site carboxylates, the FEN active site is constructed...

Neutralizing Mutations of Carboxylates That Bind Metal 2 in T5 Flap Endonuclease Result in an Enzyme That Still Requires Two Metal Ions

“…A very recent structure of hFEN1 bound to product DNA has two Sm 3ϩ ions bound in equivalent positions, and these contact the cleaved phosphate monoester (4). Despite the 8 Å distance between M1 and M2 in substratefree T5FEN structures, magnesium ion stimulation data are consistent with a mechanism where the major rate acceleration is brought about by two metal ions but where overall (k cat /K m ) has a three-divalent ion requirement (3). Thus an additional ion (M3) is bound with higher affinity to the enzyme-substrate complex.…”

“…Materials-Wild type (WT) and D201I/D204S T5FENs and 5Ј-overhanging hairpin substrate (5Ј-FAM-pd(CGCTGTC-GAACACACGCTTGCGTGTGTTC)) (HP5F) were prepared and purified to homogeneity as described (3,24,25). Divalent metal ion contaminants were removed by treatment with Chelex resin.…”

“…4E). Respective values of K I1 ϭ 7.7 Ϯ 0.9 mM (0.5 mM Mg 2ϩ ) and 40 Ϯ 18 mM (2 mM Mg 2ϩ ) were obtained by fitting the data to Equation 3. As the addition of Ca 2ϩ ions at low concentration stimulates substrate binding and the stability of complexes is similar at inhibitory concentrations, the data imply that when a substantive part of the T5FEN M2-binding site is abolished, the FEN-catalyzed reaction still requires at least two catalytically viable ions.…”

“…An unusual feature of these enzymes is their high density of active site carboxylates that coordinate essential divalent metal ion cofactors. Bacterial and bacteriophage FENs possess eight active site acidic residues, seven of which are conserved in FENs from higher organisms and also in other members of the 5Ј-nuclease superfamily (1)(2)(3)(4). In contrast, a typical metallonuclease active site consists of three or four carboxylates (5).…”

Mechanistic Studies Reveal Similar Catalytic Strategies for Phosphodiester Bond Hydrolysis by Protein-only and RNA-dependent Ribonuclease P

“…Evidence for a Two-metal Ion Mechanism-Crystal structures of metallonucleases with metals bound in the active site have fuelled mechanistic proposals for one-, two-, and even three-metal ion mechanisms (30,31). In fact, structures of PRORP1 in the presence of different divalent metal ions have revealed one (calcium) to two metal ions (manganese) bound within the active site.…”