Mechanism of NTP hydrolysis by the Escherichia coli primary replicative helicase DnaB protein. 2. Nucleotide and nucleic acid specificities

The Escherichia coli primosomal DnaT protein exists in solution as a monomer-trimer equilibrium system

The oligomerization reaction of the Escherichia coli DnaT protein has been quantitatively examined using fluorescence anisotropy and analytical ultracentrifugation methods. In solution, DnaT exists as a monomer-trimer equilibrium system. At the estimated concentration in the E. coli cell, DnaT forms a mixture of the monomer and trimer states with a 3:1 molar ratio. In spite of the modest affinity, the trimerization is a highly cooperative process, without the detectable presence of the intervening dimer. The DnaT monomer consists of a large N-terminal core domain and a small C-terminal region. The removal of the C-terminal region dramatically affects the oligomerization process. The isolated N-terminal domain forms a dimer instead of the trimer. These results indicate that the DnaT monomer possesses two structurally different, interacting sites. One site is located on the N-terminal domain, and two monomers, in the trimer, are associated through their binding sites located on that domain. The C-terminal region forms the other interacting site. The third monomer is engaged through the C-terminal regions. Surprisingly, the high affinity of the N-terminal domain dimer indicates that the DnaT monomer undergoes a conformational transition upon oligomerization, involving the C-terminal region. These data and the high specificity of the trimerization reaction, i.e., lack of any oligomers higher than a trimer, indicate that each monomer in the trimer is in contact with the two remaining monomers. A model of the global structure of the DnaT trimer based on the thermodynamic and hydrodynamic data is discussed.

DNA helicase 3.6.4.12

EC number

 3.6.4.12

Systematic name

 ATP phosphohydrolase (DNA helix unwinding)

Recommended name

 DNA helicase

Synonyms

 3’ to 5’ DNA helicase <28> [35]

 3’-5’ DNA helicase <11> [55]

 3’-5’ PfDH <11> [55]

 5’ to 3’ DNA helicase <26,27> [19,42]

 AvDH1 <47> [37]

 BACH1 helicase <19> [34]

 BLM <3> [28]

 BLM protein <3> [28]

 BRCA1-associated C-terminal helicase <19> [34]

 BcMCM <8> [52]

 CeWRN-1 <43> [9]

 DDX25 <3,48> [36]

 DNA helicase 120 <7> [15]

 DNA helicase A <4> [8]

 DNA helicase E <5> [44]

 DNA helicase II <9> [7]

 DNA helicase III <4> [27]

 DNA helicase RECQL5β <44> [17]

 DNA helicase VI <3> [45]

 Dbp9p <46> (<46> a member of the DEAD box protein family [24]) [24]

 DmRECQ5 <1> [50]

 DnaB helicase <29> [23]

 E1 helicase <17> [58]

 GRTH/DDX25 <3,48> [36]

 HCoV SF1 helicase <23> [3]

 HCoV helicase <23> [3]

 HDH IV <3> [45]

 Hel E <5> [44]

 Hmi1p <40> [60]

 MCM helicase <6,5,38> [43,54]

 MCM protein <6,35> [43]

 MER3 helicase <22> [30]

 MER3 protein <22> [30]

 MPH1 <28> [35]

 NS3 <12,50> (<12,50> ambiguous [38,65,66]) [38,65,66]

 NS3 NTPase/helicase <14> (<14> ambiguous [67]) [67]

 NS3 protein <12> (<12> ambiguous [63]) [63]

 NTPase/helicase <12,16> (<12> ambiguous [61]) [61,64]

 PDH120 <7> [15]

 PIF1 <33> [51]

 PIF1 helicase <33> [51,53]

 PcrA <37> [20]

 PcrA helicase <37,41,49> [20,21,39]

 PcrASpn <41> [21]

 PfDH A <11> [55]

 Pfh1p <27> [42]

 RECQ5 <1> [49,50]

 RECQ5 helicase <1> (<1> small isoform [49]) [49]

 RECQL5b <44> [17]

 REcQ <31> [13]

 RSF1010 RepA <30> [5]

 RecG <45> [6]

 RecQ helicase <32> [56]

 RecQsim <32> [56]

 Rep52 <24> [40]

 Rrm3p <26> [19]

 Sgs1 <36> [29]

 Sgs1 DNA helicase <36> [29]

 TWINKLE <21> [33]

 Tth UvrD <20> [16]

 UvrD <20,42> [16,22]

 UvrD helicase <39> [18]

 WRN <18> [31]

 WRN RecQ helicase <18> [12]

 WRN helicase <18> [12]

 WRN protein <18> [12]

 WRN-1 RecQ helicase <43> [9]

 Werner Syndrome helicase <18> [31]

 Werner syndrome RecQ helicase <18> [12]

 dheI I <1> [46]

 dnaB <29> [23]

 hPif1 <33> [53]

 helicase DnaB <2> [10]

 helicase II <25> [25]

 helicase PcrA <49> [39]

 helicase UvrD <20> [16]

 helicase domain of bacteriophage T7 gene 4 protein <10> [47]

 non structural protein 3 <12> (<12> ambiguous [61,62]) [61,62]

 nonstructural protein 3 <12,14,50,51> (<12,14,50> ambiguous [38,63,65,66,67]; <51> ambigous [4]) [4,38,63,65,66,67]

 protein NS3 <12> (<12> ambiguous [62]) [62]

 scHelI <4> [26]

 urvD <25> [25]

Characterization of flavonol inhibition of DnaB helicase: real-time monitoring, structural modeling, and proposed mechanism

DnaB helicases are motor proteins essential for DNA replication, repair, and recombination and may be a promising target for developing new drugs for antibiotic-resistant bacteria. Previously, we established that flavonols significantly decreased the binding ability of Klebsiella pneumoniae DnaB helicase (KpDnaB) to dNTP. Here, we further investigated the effect of flavonols on the inhibition of the ssDNA binding, ATPase activity, and dsDNA-unwinding activity of KpDnaB. The ssDNA-stimulated ATPase activity of KpDnaB was decreased to 59%, 75%, 65%, and 57%, in the presence of myricetin, quercetin, kaempferol, and galangin, respectively. The ssDNA-binding activity of KpDnaB was only slightly decreased by flavonols. We used a continuous fluorescence assay, based on fluorescence resonance energy transfer (FRET), for real-time monitoring of KpDnaB helicase activity in the absence and presence of flavonols. Using this assay, the flavonol-mediated inhibition of the dsDNA-unwinding activity of KpDnaB was observed. Modeled structures of bound and unbound DNA showed flavonols binding to KpDnaB with distinct poses. In addition, these structural models indicated that L214 is a key residue in binding any flavonol. On the basis of these results, we proposed mechanisms for flavonol inhibition of DNA helicase. The resulting information may be useful in designing compounds that target K. pneumoniae and other bacterial DnaB helicases.

The N-terminal domain of the Escherichia coli PriA helicase contains both the DNA- and nucleotide-binding sites. Energetics of domain--DNA interactions and allosteric effect of the nucleotide cofactors

Functional interactions of the Escherichia coli PriA helicase 181N-terminal domain with the DNA and nucleotide cofactors have been quantitatively examined. The isolated 181N-terminal domain forms a stable dimer in solution, most probably reflecting the involvement of the domain in specific cooperative interactions of the intact PriA protein--double-stranded DNA (dsDNA) complex. Only one monomer of the domain dimer binds the DNA; i.e., the dimer has one effective DNA-binding site. Although the total site size of the dimer--single-stranded DNA (ssDNA) complex is ~13 nucleotides, the DNA-binding subsite engages in direct interactions with approximately five nucleotides. A small number of interacting nucleotides indicates that the DNA-binding subsites of the PriA helicase, i.e., the strong subsite on the helicase domain and the weak subsite on the N-terminal domain, are spatially separated in the intact enzyme. Contrary to current views, the subsite has an only slight preference for the 3'-end OH group of the ssDNA and lacks any significant base specificity, although it has a significant dsDNA affinity. Unlike the intact helicase, the DNA-binding subsite of the isolated domain is in an open conformation, indicating the presence of the direct helicase domain--N-terminal domain interactions. The discovery that the 181N-terminal domain possesses a nucleotide-binding site places the allosteric, weak nucleotide-binding site of the intact PriA on the N-terminal domain. The specific effect of ADP on the domain DNA-binding subsite indicates that in the intact helicase, the bound ADP not only opens the DNA-binding subsite but also increases its intrinsic DNA affinity.

Inhibition of Klebsiella pneumoniae DnaB helicase by the flavonol galangin

Klebsiella pneumoniae is a ubiquitous opportunistic pathogen that colonizes at the mucosal surfaces in humans and causes severe diseases. Many clinical strains of K. pneumoniae are highly resistant to antibiotics. Here, we used fluorescence quenching to show that the flavonols galangin, myricetin, quercetin, and kaempferol, bearing different numbers of hydroxyl substituent on the aromatic rings, may inhibit dNTP binding of the primary replicative DnaB helicase of K. pneumoniae (KpDnaB), an essential component of the cellular replication machinery critical for bacterial survival. The binding affinity of KpDnaB to dNTPs varies in the following order: dCTP ~ dGTP > dTTP > dATP. Addition of 10 μM galangin significantly decreased the binding ability of KpDnaB to dATP, whereas the binding affinity of KpDnaB to dGTP that was almost unaffected. Our analyses suggest that these flavonol compounds may be used in the development of new antibiotics that target K. pneumoniae and other bacteria.

DNA Helicases

DNA and RNA helicases are organized into six superfamilies of enzymes on the basis of sequence alignments, biochemical data, and available crystal structures. DNA helicases, members of which are found in each of the superfamilies, are an essential group of motor proteins that unwind DNA duplexes into their component single strands in a process that is coupled to the hydrolysis of nucleoside 5'-triphosphates. The purpose of this DNA unwinding is to provide nascent, single-stranded DNA (ssDNA) for the processes of DNA repair, replication, and recombination. Not surprisingly, DNA helicases share common biochemical properties that include the binding of single- and double-stranded DNA, nucleoside 5'-triphosphate binding and hydrolysis, and nucleoside 5'-triphosphate hydrolysis-coupled, polar unwinding of duplex DNA. These enzymes participate in every aspect of DNA metabolism due to the requirement for transient separation of small regions of the duplex genome into its component strands so that replication, recombination, and repair can occur. In Escherichia coli, there are currently twelve DNA helicases that perform a variety of tasks ranging from simple strand separation at the replication fork to more sophisticated processes in DNA repair and genetic recombination. In this chapter, the superfamily classification, role(s) in DNA metabolism, effects of mutations, biochemical analysis, oligomeric nature, and interacting partner proteins of each of the twelve DNA helicases are discussed.

DNA structure specificity conferred on a replicative helicase by its loader

Prokaryotic and eukaryotic replicative helicases can translocate along single-stranded and double-stranded DNA, with the central cavity of these multimeric ring helicases being able to accommodate both forms of DNA. Translocation by such helicases along single-stranded DNA results in the unwinding of forked DNA by steric exclusion and appears critical in unwinding of parental strands at the replication fork, whereas translocation over double-stranded DNA has no well-defined role. We have found that the accessory factor, DnaC, that promotes loading of the Escherichia coli replicative helicase DnaB onto single-stranded DNA may also act to confer DNA structure specificity on DnaB helicase. When present in excess, DnaC inhibits DnaB translocation over double-stranded DNA but not over single-stranded DNA. Inhibition of DnaB translocation over double-stranded DNA requires the ATP-bound form of DnaC, and this inhibition is relieved during translocation over single-stranded DNA indicating that stimulation of DnaC ATPase is responsible for this DNA structure specificity. These findings demonstrate that DnaC may provide the DNA structure specificity lacking in DnaB, limiting DnaB translocation to bona fide replication forks. The ability of other replicative helicases to translocate along single-stranded and double-stranded DNA raises the possibility that analogous regulatory mechanisms exist in other organisms.