Five‐stranded β‐sheet sandwiched with two α‐helices: A structural link between restriction endonucleases <i>Eco</i>RI and <i>Eco</i>RV

Venclovas, C̆eslovas; Timinskas, Albertas; Šikšnys, Virginijus

doi:10.1002/prot.340200308

Cited by 63 publications

(54 citation statements)

References 13 publications

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“…As shown in Fig. 8, the structural core, which is characteristic for many type II restriction endonucleases (7,8,62), is likely to be also present in SsoII and EcoRII. Projected onto this structural core, the presumptive functionally important amino acid residues are found in similar locations as observed in NgoMIV, if one takes into account that the borders of individual secondary structure elements are not easily predicted.…”

Section: Discussionmentioning

confidence: 99%

Evolutionary Relationship between Different Subgroups of Restriction Endonucleases

Pingoud¹,

Кубарева²,

Stengel³

et al. 2002

Journal of Biological Chemistry

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The type II restriction endonuclease SsoII shows sequence similarity with 10 other restriction endonucleases, among them the type IIE restriction endonuclease EcoRII, which requires binding to an effector site for efficient DNA cleavage, and the type IIF restriction endonuclease NgoMIV, which is active as a homotetramer and cleaves DNA with two recognition sites in a concerted reaction. We show here that SsoII is an orthodox type II enzyme, which is active as a homodimer and does not require activation by binding to an effector site. Nevertheless, it shares with EcoRII and NgoMIV a very similar DNA-binding site and catalytic center as shown here by a mutational analysis, indicative of an evolutionary relationship between these three enzymes. We suggest that a similar relationship exists between other orthodox type II, type IIE, and type IIF restriction endonucleases. This may explain why similarities may be more pronounced between members of different subtypes of restriction enzymes than among the members of a given subtype.More than 3000 different type II restriction endonucleases are known and characterized with respect to their cleavage specificities (1). This group of enzymes probably constitutes one of the largest families of enzymes with the same basic function. This makes type II restriction endonucleases (like DNA methyltransferases) ideal objects to study evolutionary relationships. Moreover, in principle, the family relationships should eventually allow predicting structural and functional features of an individual restriction endonuclease, solely on the basis of sequence comparisons. This was not obvious for a long time since only 10 years ago restriction endonucleases, because of their little sequence conservation, were not considered to be related in evolution (2, 3). But this changed due to the progress made in the analysis of sequence similarities (4 -6) and, in particular, due to the increasing number of crystal structures of restriction enzymes (reviewed in Refs. 7 and 8), which made it obvious that these enzymes have very similar structural cores. Nevertheless, it has been shown recently that some genuine restriction enzymes belong to distinct nuclease superfamilies (Nuc, HNH, and GIY-YIG), which are unrelated and structurally dissimilar to each other and to the "archetypal" (P)D . . . (D/E)XK superfamily (9 -11). These findings make comparative studies using sequences of restriction enzymes even more challenging.We have begun to study the restriction endonuclease SsoII recently (12-15). It is a type II enzyme (reviewed in Refs. 8 and 16) composed of identical subunits each consisting of 305 amino acid residues (17). It cleaves the palindromic sequence 2CC-NGG in the presence of Mg 2ϩ as indicated (18). Our interest in studying this enzyme is due to its sequence similarity to Eco-RII, a type IIE enzyme (reviewed in Ref. 19), which being somewhat larger than SsoII is a dimer of identical subunits each consisting of 404 amino acid residues (20, 21). As a type IIE enzyme EcoRII has two DNA-binding...

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Section: Discussionmentioning

confidence: 99%

Evolutionary Relationship between Different Subgroups of Restriction Endonucleases

Pingoud¹,

Кубарева²,

Stengel³

et al. 2002

Journal of Biological Chemistry

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“…The overall folds of EcoRI and BamHI as well as parts of the folds of EcoRV and PvulI are similar [8]. All four enzymes have a central five stranded B-sheet which harbours the catalytic centre composed of three homologous amino acid residues [9]. In the cocrystal structures these residues (Asp-91, Glu-lll and Lys-ll3 in EcoRI, Asp-74, Asp-90 and Lys-92 in EcoRV, Asp-58, Glu-68 and Lys-70 in PvuII and Asp-94, Glu-lll and Glu-ll3 in BamHI) are in a similar position relative to the phosphodiester bond to be cleaved ( Fig.…”

Section: Introductionmentioning

confidence: 99%

Asp‐59 is not important for the catalytic activity of the restriction endonuclease EcoRI

1996

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“…The active sites of the type II enzymes have a signature sequence PD(X) n DXK, in which four residues (Pro, Asp, Asp, and Lys; n ϭ 1 (PvuII) to ϳ49 (Bse634I) (2)) are weakly conserved and two separated acidic residues are usually followed by a basic residue. The active site structures thus share a common structural motif consisting of a five-stranded ␤-sheet flanked with ␣-helices (3)(4)(5). Specific divalent metal cations such as Mg 2ϩ are required to express the enzymatic activities and are coordinated to the conserved acidic residues during the catalytic reaction.…”

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confidence: 99%

Crystal Structures of Type II Restriction Endonuclease EcoO109I and Its Complex with Cognate DNA

Hashimoto

Shimizu

Imasaki

et al. 2005

Journal of Biological Chemistry

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EcoO109I is a type II restriction endonuclease that recognizes the DNA sequence of RGGNCCY. Here we describe the crystal structures of EcoO109I and its complex with DNA. A comparison of the two structures shows that the catalytic domain moves drastically to capture the DNA. One metal ion and two water molecules are observed near the active site of the DNA complex. The metal ion is a Lewis acid that stabilizes the pentavalent phosphorus atom in the transition state. One water molecule, activated by Lys-126, attacks the phosphorus atom in an S N 2 mechanism, whereas the other water interacts with the 3-leaving oxygen to donate a proton to the oxygen. EcoO109I is similar to EcoRI family enzymes in terms of its DNA cleavage pattern and folding topology of the common motif in the catalytic domain, but it differs in the manner of DNA recognition. Our findings propose a novel classification of the type II restriction endonucleases and lead to the suggestion that EcoO109I represents a new subclass of the EcoRI family.Bacteria have evolved a mechanism to protect themselves from viral infection. Restriction endonucleases (REases) 1 provide an anti-viral protection for bacteria by degrading the foreign DNA of invading bacteriophages. The enzymes recognize specific nucleotide sequences and cleave both strands of DNA. To date, more than 3,500 REases have been characterized and classified into four types, I, II, III, and IV (1). Of these types, type II REases are widely used in genetic technology and are the most well studied.Type II REases generally recognize 4 -8 base pairs of doublestranded DNA and hydrolyze phosphodiester bonds within the recognition sequences. The amino acid sequences are not homologous with the exception of the active site sequence. The active sites of the type II enzymes have a signature sequence PD(X) n DXK, in which four residues (Pro, Asp, Asp, and Lys; n ϭ 1 (PvuII) to ϳ49 (Bse634I) (2)) are weakly conserved and two separated acidic residues are usually followed by a basic residue. The active site structures thus share a common structural motif consisting of a five-stranded ␤-sheet flanked with ␣-helices (3-5). Specific divalent metal cations such as Mg 2ϩ are required to express the enzymatic activities and are coordinated to the conserved acidic residues during the catalytic reaction. However, details of the mechanism of the catalytic reaction are not fully understood (2).Type II REases have been classified into two families, EcoRI and EcoRV, based on their DNA cleavage pattern. The EcoRI family produces 5Ј-overhang DNA, whereas the EcoRV family produces blunt-end DNA. From a structural viewpoint, the EcoRI family approaches DNA from the major groove side, whereas the EcoRV family approaches from the minor groove side. Moreover, the folding topology of the five-stranded ␤-sheet in the common structural motif in the active site differs between the two families (7) where the topology of four ␤-strands are absolutely conserved in the common motif but the fifth ␤-strand is oppositely oriented (8).To ...

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Five‐stranded β‐sheet sandwiched with two α‐helices: A structural link between restriction endonucleases EcoRI and EcoRV

Cited by 63 publications

References 13 publications

Evolutionary Relationship between Different Subgroups of Restriction Endonucleases

Evolutionary Relationship between Different Subgroups of Restriction Endonucleases

Asp‐59 is not important for the catalytic activity of the restriction endonuclease EcoRI

Crystal Structures of Type II Restriction Endonuclease EcoO109I and Its Complex with Cognate DNA

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