The exceptionally tight affinity of DnaA for ATP/ADP requires a unique aspartic acid residue in the AAA+ sensor 1 motif

Kawakami, Hironori; Ozaki, Shogo; Suzuki, Shigeo; Nakamura, Kenta; Senriuchi, Takayuki; Su’etsugu, Masayuki; Fujimitsu, Kazuyuki; Katayama, Tsutomu

doi:10.1111/j.1365-2958.2006.05450.x

Cited by 38 publications

(82 citation statements)

References 61 publications

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“…Previously, we demonstrated that the DnaA N-terminal domains I-II bind to DiaA (Ishida et al 2004). Domain III and the C-terminal domain IV of DnaA are associated with ATP/ADP-binding and DNA-binding activities, respectively (Erzberger et al 2002;Messer 2002;Fujikawa et al 2003;Kawakami et al 2005Kawakami et al , 2006Kaguni 2006). DiaA stimulated the formation of DnaA multimers on oriC, which stimulated the formation of open complexes.…”

Section: Discussionmentioning

confidence: 99%

“…We next performed a P1 nuclease assay to investigate whether DiaA promoted the formation of the oriC open complex (Kawakami et al , 2006. P1 nuclease specifically degrades single-stranded DNA.…”

Section: Diaa Stimulates Open Complex Formationmentioning

confidence: 99%

“…The gel-mobility assay was performed as previously described (Kawakami et al 2006;Ozaki et al 2006). Briefly, DnaA was incubated for 20 min on ice in buffer (10 µL) containing 2 mM ATP and the 15-mer DnaA R1 box (2.5 pmol) in the presence or absence of hisDiaA (20 pmol).…”

Section: Gel-mobility Retardation Assaymentioning

confidence: 99%

“…The P1 nuclease assay was performed as previously described (Kawakami et al 2006;Ozaki et al 2006). Briefly, the indicated amounts of hisDiaA were incubated for 3 min at 38°C in buffer DiaA mediates ATP-DnaA initiation complex…”

Section: Open Complex Formation Assay Using P1 Nucleasementioning

confidence: 99%

“…Flow cytometry was performed as described previously with minor modifications (Kawakami et al 2006). Briefly, cells were exponentially grown for ∼10 generations at 30°C, followed by incubation in the presence of rifampicin (300 µg/mL) and cephalexin (10 µg/mL) for an additional 4 h. Cells were collected in cold 70% ethanol, washed, and resuspended in cold buffer containing 10 mM Tris-HCl (pH 7.5), 10 mM magnesium sulfate, and 2 µM SYTOX green (Invtrogen), then analyzed using a FACScalibur flow cytometry system (Becton Dickinson).…”

Section: Flow Cytometry Analysismentioning

confidence: 99%

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The interaction of DiaA and DnaA regulates the replication cycle in E. coli by directly promoting ATP–DnaA-specific initiation complexes

Keyamura¹,

Fujikawa

Ishida³

et al. 2007

Genes Dev.

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118

192

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Escherichia coli DiaA is a DnaA-binding protein that is required for the timely initiation of chromosomal replication during the cell cycle. In this study, we determined the crystal structure of DiaA at 1.8 Å resolution. DiaA forms a homotetramer consisting of a symmetrical pair of homodimers. Mutational analysis revealed that the DnaA-binding activity and formation of homotetramers are required for the stimulation of initiation by DiaA. DiaA tetramers can bind multiple DnaA molecules simultaneously. DiaA stimulated the assembly of multiple DnaA molecules on oriC, conformational changes in ATP-DnaA-specific initiation complexes, and unwinding of oriC duplex DNA. The mutant DiaA proteins are defective in these stimulations. DiaA associated also with ADP-DnaA, and stimulated the assembly of inactive ADP-DnaAoriC complexes. Specific residues in the putative phosphosugar-binding motif of DiaA were required for the stimulation of initiation and formation of ATP-DnaA-specific-oriC complexes. Our data indicate that DiaA regulates initiation by a novel mechanism, in which DiaA tetramers most likely bind to multiple DnaA molecules and stimulate the assembly of specific ATP-DnaA-oriC complexes. These results suggest an essential role for DiaA in the promotion of replication initiation in a cell cycle coordinated manner.[Keywords: initiation of replication; protein complex; complex structure; DNA dynamics; cell cycle regulation; initiator regulation] Supplemental material is available at http://www.genesdev.org.

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Section: Discussionmentioning

confidence: 99%

Section: Diaa Stimulates Open Complex Formationmentioning

confidence: 99%

Section: Gel-mobility Retardation Assaymentioning

confidence: 99%

Section: Open Complex Formation Assay Using P1 Nucleasementioning

confidence: 99%

Section: Flow Cytometry Analysismentioning

confidence: 99%

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The interaction of DiaA and DnaA regulates the replication cycle in E. coli by directly promoting ATP–DnaA-specific initiation complexes

Keyamura¹,

Fujikawa

Ishida³

et al. 2007

Genes Dev.

Self Cite

118

192

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X‐ray crystal structure of Escherichia coli HspQ, a protein involved in the retardation of replication initiation

et al. 2017

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The heat shock protein HspQ (YccV) of Escherichia coli has been proposed to participate in the retardation of replication initiation in cells with the dnaA508 allele. In this study, we have determined the 2.5-Å-resolution X-ray structure of the trimer of HspQ, which is also the first structure of a member of the YccV superfamily. The acidic character of the HspQ trimer suggests an interaction surface with basic proteins. From these results, we discuss the cellular function of HspQ, including its relationship with the DnaA508 protein.

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ATP ‐binding Motifs

Matte

Delbaere

2010

Encyclopedia of Life Sciences

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Adenosine 5′‐triphosphate (ATP) binds to a great number of proteins to elicit a wide variety of effects, including energy production and molecular signalling. Proteins have evolved different strategies to specifically recognize ATP, utilizing different ways of binding the phosphoryl moieties as well as the adenine base. The most common, conserved sequence and structural motif for binding ATP is the Walker‐A motif, or P‐loop, found in many different protein structural families. Greater variation in the sequence of the P‐loop is being recognized, as more ATP‐binding proteins are being structurally and functionally characterized. In contrast to the P‐loop, recognition of the adenine base often makes use of conserved structural motifs of main‐chain atoms via hydrogen‐bonding interactions, or side‐chains in stacking interactions, without a definitive amino acid sequence pattern. Key concepts: A major class of ATP‐binding proteins are those that contain a P‐loop or Walker‐A motif. P‐loops or glycine‐rich loops function by binding the phosphoryl groups of ATP. Several sequence variations on the Walker‐A motif are now known and have been functionally characterized. The Walker‐B motif contains a conserved acidic residue (Glu/Asp) that functions to bind directly or indirectly a metal ion important in catalysis. Adenine‐binding does not occur through specific sequence motifs, but rather uses a conserved pattern of polar and nonpolar interactions within a structural motif. Both main‐chain hydrogen bonding and aromatic residue stacking contribute to adenine‐binding by proteins.

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The exceptionally tight affinity of DnaA for ATP/ADP requires a unique aspartic acid residue in the AAA+ sensor 1 motif

Cited by 38 publications

References 61 publications

The interaction of DiaA and DnaA regulates the replication cycle in E. coli by directly promoting ATP–DnaA-specific initiation complexes

The interaction of DiaA and DnaA regulates the replication cycle in E. coli by directly promoting ATP–DnaA-specific initiation complexes

X‐ray crystal structure of Escherichia coli HspQ, a protein involved in the retardation of replication initiation

ATP ‐binding Motifs

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