Functional domains of DnaA proteins

Messer, Walter; Blaesing, Franca; Majka, Jerzy; Nardmann, Judith; Schaper, Sigrid; Schmidt, Andrea; Seitz, Harald; Speck, Christian; Tüngler, Doreen; Węgrzyn, Grzegorz; Weigel, Christoph; Welzeck, Michaela; Zakrzewska‐Czerwińska, Jolanta

doi:10.1016/s0300-9084(99)00215-1

Cited by 91 publications

(100 citation statements)

References 46 publications

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“…These data are consistent with this segment functioning as a flexible linker between domain I and the ATPase and HTH domains [4]. A search for structural homologs [49] revealed that the N-terminal domain is similar to ribosomal binding factor A (RbfA) [50,51], which contains a type II KH RNAbinding fold (Z score of 3-4).…”

Section: Page 7 12/12/06supporting

confidence: 63%

Section: Page 7 12/12/06supporting

confidence: 62%

“…The three-dimensional structure is formed by the packing of helices I and IV and II and III against one another and one side of the β-sheet, while helix V packs against the opposite face ( Figure 3). As mentioned previously, the last fifteen residues of the construct, which correspond to the first residues of domain II [4], show no long-ranges NOEs, suggesting that they are unstructured.These data are consistent with this segment functioning as a flexible linker between domain I and the ATPase and HTH domains [4]. A search for structural homologs [49] revealed that the N-terminal domain is similar to ribosomal binding factor A (RbfA) [50,51], which contains a type II KH RNAbinding fold (Z score of 3-4).…”

supporting

confidence: 63%

“…In this Page 4 12/12/06 construct an N-terminal methionine and six glycine residues precede the first methionine of DnaA.…”

Section: Methodsmentioning

confidence: 99%

“…ATP hydrolysis acts as the switch between active (ATP-bound) and inactive (ADP-bound) forms of DnaA. Initiation begins only with the ATP-bound form (for reviews see [2][3][4] , as well as domain IV bound to DNA [8] showed that domain III resembles other members of the AAA+ family of ATPases, and that domain IV adopts a helix-turn-helix DNA-binding fold. In contrast, the secondary structure of domain I has been predicted based on multiple sequence alignments [5,9,10], however, little is known about its tertiary structure.…”

mentioning

confidence: 99%

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NMR structure of the N-terminal domain of the replication initiator protein DnaA

Lowery

Chandonia

Kim

et al. 2007

J Struct Funct Genomics

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DnaA is an essential component in the initiation of bacterial chromosomal replication. DnaA binds to a series of 9 base pair repeats leading to oligomerization, recruitment of the DnaBC helicase, and the assembly of the replication fork machinery. The structure of the N-terminal domain (residues 1 -100) of DnaA from Mycoplasma genitalium was determined by NMR spectroscopy. The backbone r.m.s.d. for the first 86 residues was 0.6 +/-0.2 Å based on 742 NOE, 50 hydrogen bond, 46 backbone angle, and 88 residual dipolar coupling restraints. Ultracentrifugation studies revealed that the domain is monomeric in solution. Features on the protein surface include a hydrophobic cleft flanked by several negative residues on one side, and positive residues on the other. A negatively charged ridge is present on the opposite face of the protein. These surfaces may be important sites of interaction with other proteins involved in the replication process. Together, the structure and NMR assignments should facilitate the design of new experiments to probe the protein-protein interactions essential for the initiation of DNA replication.Keywords: replication, DnaB, DiaA, ATPase, initiation Page 2 12/12/06The bacterial protein DnaA plays a central role in the initiation of chromosomal replication and is involved in the activation and repression of several genes, including its own gene (dnaA) in E.coli. Replication begins with the formation of oligomers of DnaA on recognition sites at the origin of replication (OriC). The DnaA complex unwinds and opens several AT-rich segments of doublestranded DNA within the origin and stabilizes the resulting single-strands. DnaA then recruits the DnaB helicase with help from DnaC to form the "prepriming complex" [1]. After priming of the singlestranded DNA, replication occurs by the action of DNA Polymerase III. ATP hydrolysis acts as the switch between active (ATP-bound) and inactive (ADP-bound) forms of DnaA. Initiation begins only with the ATP-bound form (for reviews see [2][3][4] , as well as domain IV bound to DNA [8] showed that domain III resembles other members of the AAA+ family of ATPases, and that domain IV adopts a helix-turn-helix DNA-binding fold. In contrast, the secondary structure of domain I has been predicted based on multiple sequence alignments [5,9,10], however, little is known about its tertiary structure.DnaA recognizes five high affinity 9 base pair sites as well as several lower affinity 6 base pair sites within OriC via the C-terminal helix-turn-helix DNA-binding domain (domain IV) [11,12]. In addition to direct binding, the formation of oligomers containing 20 to 30 molecules of DnaA at the origin has been demonstrated by electron microscopy [13,14]. The mechanism of oligomer formation has been studied extensively [3,15], but the nature of the complex remains poorly understood.Replacement of the dimerization domain of the lambda cI repressor with the N-terminal domain of DnaA resulted in a functional chimeric protein, suggesting direct interactions between the N-terminal ...

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