Crystal structure of Penicillium citrinum P1 nuclease at 2.8 A resolution.

Volbeda, Anne; Lahm, Armin; Sakiyama, Fumio; Suck, Dietrich

doi:10.1002/j.1460-2075.1991.tb07683.x

Cited by 262 publications

(210 citation statements)

References 41 publications

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“…A similar example of evolutionary relationship was reported by Volbeda et al (1991). They found a distant evolutionary relationship between two phosphodiesterases, B. cereus PC-PLC (Hough et al, 1989) and Penicillium citrinum PI nuclease (Lahm et al, 1990;Volbeda et al, 1991).…”

Section: Evolutionary Relationship Between Smase and Dnase Isupporting

confidence: 64%

“…They found a distant evolutionary relationship between two phosphodiesterases, B. cereus PC-PLC (Hough et al, 1989) and Penicillium citrinum PI nuclease (Lahm et al, 1990;Volbeda et al, 1991). The two enzymes show no significant overall sequence similarity, but their known three-dimensional structures and catalytically important residues are well conserved (Volbeda et al, 1991).…”

Section: Evolutionary Relationship Between Smase and Dnase Imentioning

confidence: 99%

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A distant evolutionary relationship between bacterial sphingomyelinase and mammalian DNase I

et al. 1996

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The three-dimensional structure of bacterial sphingomyelinase (SMase) was predicted using a protein fold recognition method; the search of a library of known structures showed that the SMase sequence is highly compatible with the mammalian DNase I structure, which suggested that SMase adopts a structure similar to that of DNase I. The amino acid sequence alignment based on the prediction revealed that, despite the lack of overall sequence similarity (less than 10% identity), those residues of DNase I that are involved in the hydrolysis of the phosphodiester bond, including two histidine residues (His 134 and His 252) of the active center, are conserved in SMase. In addition, a conserved pentapeptide sequence motif was found, which includes two catalytically critical residues, Asp 251 and His 252. A sequence database search showed that the motif is highly specific to mammalian DNase I and bacterial SMase. The functional roles of SMase residues identified by the sequence comparison were consistent with the results from mutant studies. Two Bacillus cereus SMase mutants (H134A and H252A) were constructed by site-directed mutagenesis. They completely abolished their catalytic activity. A model for the SMase-sphingomyelin complex structure was built to investigate how the SMase specifically recognizes its substrate. The model suggested that a set of residues conserved among bacterial SMases, including Trp 28 and Phe 55, might be important in the substrate recognition. The predicted structural similarity and the conservation of the functionally important residues strongly suggest a distant evolutionary relationship between bacterial SMase and mammalian DNase I. These two phosphodiesterases must have acquired the specificity for different substrates in the course of evolution.

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Section: Evolutionary Relationship Between Smase and Dnase Isupporting

confidence: 64%

Section: Evolutionary Relationship Between Smase and Dnase Imentioning

confidence: 99%

A distant evolutionary relationship between bacterial sphingomyelinase and mammalian DNase I

et al. 1996

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“…In the E7 structure this site is occupied by water, while phosphate is found in E9. Water coordination to the metal points to its possible activation to produce hydroxide, in a fashion similar to other hydrolytic zinc enzymes such as the single strand-dependent nuclease P1, where the hydroxide produced is postulated to attack the scissile phosphodiester bond (38). However, we see no significant zinc or nickel-dependent endonuclease activity for the colicin E9 DNase using double-stranded DNA substrates, in both plasmid nicking assays (Fig.…”

Section: Zinc Is the Physiological Metal For Colicin Endonucleases-supporting

confidence: 50%

Homing in on the Role of Transition Metals in the HNH Motif of Colicin Endonucleases

Pommer

Kühlmann

Cooper

et al. 1999

Journal of Biological Chemistry

123

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The cytotoxic domain of the bacteriocin colicin E9 (the E9 DNase) is a nonspecific endonuclease that must traverse two membranes to reach its cellular target, bacterial DNA. Recent structural studies revealed that the active site of colicin DNases encompasses the HNH motif found in homing endonucleases, and bound within this motif a single transition metal ion (either Zn 2؉ or Ni 2؉ ) the role of which is unknown. In the present work we find that neither Zn 2؉ nor Ni 2؉ is required for DNase activity, which instead requires Mg 2؉ ions, but binding transition metals to the E9 DNase causes subtle changes to both secondary and tertiary structure. Spectroscopic, proteolytic, and calorimetric data show that, accompanying the binding of 1 eq of Zn 2؉ , Ni 2؉ , or Co 2؉ , the thermodynamic stability of the domain increased substantially, and that the equilibrium dissociation constant for Zn 2؉ was less than or equal to nanomolar, while that for Co 2؉ and Ni 2؉ was micromolar. Our data demonstrate that the transition metal is not essential for colicin DNase activity but rather serves a structural role. We speculate that the HNH motif has been adapted for use by endonuclease colicins because of its involvement in DNA recognition and because removal of the bound metal ion destabilizes the DNase domain, a likely prerequisite for its translocation across bacterial membranes.Colicins are a formidable weapon in the armory of a bacterium as it competes for nutrients with other bacteria, exemplified by the first-order kinetics of colicin-mediated cell death, which imply that a single toxin molecule is sufficient to kill a cell (1). Colicins have been intensively studied since the late 1950s (2), with much of this work revolving around how these folded proteins are able to traverse the membrane barriers of a bacterium (reviewed in Ref. 3). This process is distinct from that of mitochondrial import in eukaryotic cells since colicins do not possess signal sequences but rather are dependent on the activities of three domains: a central receptor recognition domain involved in binding to outer membrane nutrient receptors; an N-terminal translocation domain, which, through its interactions with several periplasmic proteins, causes the outer membrane to be breached allowing the C-terminal cytotoxic domain to enter the periplasm. This latter activity is most often a voltage-gated ionophore (colicins A, B, Ia, E1, and N, for example), which associates with the inner membrane as a molten globule, and then depolarizes the cell (4 -6). Cell death ensues through the efflux of potassium and other ions out of the cell.Of the many different types of colicin that have been identified, perhaps the most unusual are the nuclease family of E colicins (reviewed in Ref. 7). Nuclease colicins require the outer membrane vitamin B 12 receptor BtuB as well as the porin OmpF and the Tol proteins (located in both the periplasm and inner membrane) for import. This complex machinery is needed to translocate the cytotoxic domain across both membranes of Esche...

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“…Even in the case of nucleases, there are indications for the existence of subsites. For nuclease P1, two mononulceotide-binding sites have been identified [34]. Although the above-mentioned enzymes d o not catalyse a transesterification reaction, the kinetic mechanism presented in this paper may be an appropriate formalism to describe/rationalise the efficient use of subsite binding energy in turnover for other depolymerizing enzymes including ribonucleases, nucleases, glycosidases and protease…”

Section: Steady-state Treatment Of the Two-binding-site Model So Farmentioning

confidence: 99%

A Two‐Binding‐Site Kinetic Model for the Ribonuclease‐T₁‐Catalysed Transesterification of Dinucleoside Phosphate Substrates

Steyaert

Engelborghs

1995

European Journal of Biochemistry

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Ribonucleases have been found to have subsites that confer large rate enhancements but do not contribute to substrate binding. In this study, we present a kinetic model that formally explains how subsite binding energy is converted into chemical activation energy. The proposed mechanism takes into account a primary specificity site and a subsite, both of which must be occupied for chemical turnover. An unstable reaction intermediate is formed upon binding of the polymeric substrate monomers at the corresponding subsites. The structure of this reaction intermediate resembles the transition state of the catalysed transphosphorylation reaction. Similar mechanisms may be used by other depolymerizing enzymes including nucleases, glycosidases, and proteases.Keywords: ribonuclease T, ; subsite ; enzyme kinetics.It is well established that enzymes degrading polymeric substrates contain subsites for secondary substrate units, the interaction being mostly used to increase turnover rather than to bind the substrate [I]. Ribonucleases are no exception in this regard. For bovine pancreatic ribonuclease, a member of the super family of pyrimidine-specific ribonucleases [ 21, the transesterification rates of CpN and UpN (3',5'-linked dinucleoside monophosphate compounds) were shown to vary by more than 100-fold depending on the nature of N, whereas the Michaelis constants Ahhreviations. GfpC, 2'-deoxy-2'-tluoroguanylyl-(3'-S')-cytidine; 2'-GMP, 2'-guanylic acid; 3'-GMP, 3'-guanylic acid ; 5'-GMP, 5'-guanylic acid; 2',5'-GpG, guanylyI-[2'-5')-guanosine; GpMe. guanosine-3'-(methyl phosphate); NpN, 3'Slinked dinucleoside monophosphate compounds (N represents any of the four common nucleosides); RNase, ribonuclease.Enzymes. Barnase (EC 3.1.27.-): elastase (EC 3.4.21.36); lysozyme (EC 3.2.1.17): ribonuclease A (EC 3.1.27.5); ribonuclease Ms (EC 3.1.27.1): ribonuclease T, (EC 3.1.27.3).In this study, we present a simple kinetic model that may explain how ribonucleases use a low-affinity subsite to depolymerize RNA. The model considers a primary specificity site and a subsite, both of which must be occupied to form an active enzymehbstrate complex. The formalism presented here is consistent with the kinetic properties of most ribonucleases and is useful for analysis of the kinetic properties of subsite binding. RESULTSKinetics of the two-binding-site model. Let us consider the following general two-binding-site model (Fig. 1 ) considering random binding at the primary site and the subsite to analyse the ribonuclease-catalysed cleavage of any dinucleoside phosphate substrate A-B. This general reaction scheme involves three central complexes. ES,,,,,,, represents those enzyme substrate complexes in which the primary site is occupied with the upstream nucleotide A. In ES,,,,, the substrate leaving group B is bound to the subsite. ES represents the enzyme/substrate complex in which both the primary site and the subsite are occupied. This system is defined by the following equilibrium constants:

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Crystal structure of Penicillium citrinum P1 nuclease at 2.8 A resolution.

Cited by 262 publications

References 41 publications

A distant evolutionary relationship between bacterial sphingomyelinase and mammalian DNase I

A distant evolutionary relationship between bacterial sphingomyelinase and mammalian DNase I

Homing in on the Role of Transition Metals in the HNH Motif of Colicin Endonucleases

A Two‐Binding‐Site Kinetic Model for the Ribonuclease‐T₁‐Catalysed Transesterification of Dinucleoside Phosphate Substrates

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Crystal structure of Penicillium citrinum P1 nuclease at 2.8 A resolution.

Cited by 262 publications

References 41 publications

A distant evolutionary relationship between bacterial sphingomyelinase and mammalian DNase I

A distant evolutionary relationship between bacterial sphingomyelinase and mammalian DNase I

Homing in on the Role of Transition Metals in the HNH Motif of Colicin Endonucleases

A Two‐Binding‐Site Kinetic Model for the Ribonuclease‐T1‐Catalysed Transesterification of Dinucleoside Phosphate Substrates

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Product

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A Two‐Binding‐Site Kinetic Model for the Ribonuclease‐T₁‐Catalysed Transesterification of Dinucleoside Phosphate Substrates