Structure and Function of DnaA N-terminal Domains

DnaA forms a homomultimeric complex with the origin of chromosomal replication (oriC) to unwind duplex DNA. The interaction of the DnaA N terminus with the DnaB helicase is crucial for the loading of DnaB onto the unwound region. Here, we determined the DnaA N terminus structure using NMR. This region (residues 1–108) consists of a rigid region (domain I) and a flexible region (domain II). Domain I has an α-α-β-β-α-β motif, similar to that of the K homology (KH) domain, and has weak affinity for oriC single-stranded DNA, consistent with KH domain function. A hydrophobic surface carrying Trp-6 most likely forms the interface for domain I dimerization. Glu-21 is located on the opposite surface of domain I from the Trp-6 site and is crucial for DnaB helicase loading. These findings suggest a model for DnaA homomultimer formation and DnaB helicase loading on oriC. DnaA forms a homomultimeric complex with the origin of chromosomal replication (oriC) to unwind duplex DNA. The interaction of the DnaA N terminus with the DnaB helicase is crucial for the loading of DnaB onto the unwound region. Here, we determined the DnaA N terminus structure using NMR. This region (residues 1–108) consists of a rigid region (domain I) and a flexible region (domain II). Domain I has an α-α-β-β-α-β motif, similar to that of the K homology (KH) domain, and has weak affinity for oriC single-stranded DNA, consistent with KH domain function. A hydrophobic surface carrying Trp-6 most likely forms the interface for domain I dimerization. Glu-21 is located on the opposite surface of domain I from the Trp-6 site and is crucial for DnaB helicase loading. These findings suggest a model for DnaA homomultimer formation and DnaB helicase loading on oriC. In Escherichia coli, DnaA initiates the replication of genomic DNA in a cell cycle-coordinated manner (1Kaguni J.M. Annu. Rev. Microbiol. 2006; 60: 351-375Crossref PubMed Scopus (165) Google Scholar, 2Messer W. FEMS Microbiol. Rev. 2002; 26: 355-374PubMed Google Scholar). The initiation complex contains a homomultimer of DnaA protein and the replication origin, oriC, of the chromosome. DnaA binds cooperatively to the oriC region in a manner depending on tight binding to the DnaA box sequences within the oriC region. The initiation complex containing ATP-bound DnaA molecules unwinds the duplex of the AT-rich 13-mer repeats within oriC, forming an open complex. This leads to the loading of DnaB helicase onto single-stranded DNA (ssDNA) 4The abbreviations used are: ssDNA, single-stranded DNA; HSQC, heteronuclear single quantum correlation; KH, K homology; NOE, nuclear Overhauser enhancement; NOESY, NOE spectroscopy; PCBP2, poly(C)-binding protein 2; PDB, Protein Data Bank; RIDA, regulatory inactivation of DnaA; r.m.s.d., root mean square deviation; WT, wild type. in the presence of the DnaC helicase loader. In this process, the interaction between DnaA and DnaB is crucial. DnaA creates a specific nucleoprotein structure within which ordered structural DNA changes and protein-protein interactions take place. DnaG primase then complexes with the ssDNA-loaded DnaB, which leads to DNA chain synthesis by the DNA polymerase III holoenzyme. The DNA-loaded β-clamp subunit of the holoenzyme complexes with Hda, a DnaA paralogue protein, and this complex promotes DnaA-ATP hydrolysis, yielding inactive ADP-DnaA (3Katayama T. Kubota T. Kurokawa K. Crooke E. Sekimizu K. Cell. 1998; 94: 61-71Abstract Full Text Full Text PDF PubMed Scopus (263) Google Scholar, 4Kato J. Katayama T. EMBO J. 2001; 20: 4253-4262Crossref PubMed Scopus (217) Google Scholar, 5Su'etsugu M. Shimuta T.R. Ishida T. Kawakami H. Katayama T. J. Biol. Chem. 2005; 280: 6528-6536Abstract Full Text Full Text PDF PubMed Scopus (82) Google Scholar). DnaA is a 52-kDa basic protein that has four distinct functional domains (1Kaguni J.M. Annu. Rev. Microbiol. 2006; 60: 351-375Crossref PubMed Scopus (165) Google Scholar, 2Messer W. FEMS Microbiol. Rev. 2002; 26: 355-374PubMed Google Scholar). NMR and crystal structure analyses have revealed that C-terminal domain IV of E. coli DnaA has a helix-turn-helix motif, which binds the DnaA box specifically (6Fujikawa N. Kurumizaka H. Nureki O. Terada T. Shirouzu M. Katayama T. Yokoyama S. Nucleic Acids Res. 2003; 31: 2077-2086Crossref PubMed Scopus (147) Google Scholar, 7Obita T. Iwura T. Su'etsugu M. Yoshida Y. Tanaka Y. Katayama T. Ueda T. Imoto T. Biochem. Biophys. Res. Commun. 2002; 299: 42-48Crossref PubMed Scopus (17) Google Scholar, 8Yoshida Y. Obita T. Kokusho Y. Ohmura T. Katayama T. Ueda T. Imoto T. Cell. Mol. Life Sci. 2003; 60: 1998-2008Crossref PubMed Scopus (9) Google Scholar). DnaA domain III contains ATP binding/hydrolysis motifs of the AAA+ ATPase family (9Erzberger J.P. Mott M.L. Berger J.M. Nat. Struct. Mol. Biol. 2006; 13: 676-683Crossref PubMed Scopus (236) Google Scholar, 10Erzberger J.P. Pirruccello M.M. Berger J.M. EMBO J. 2002; 21: 4763-4773Crossref PubMed Scopus (193) Google Scholar, 11Hanson P.I. Whiteheart S.W. Nat. Rev. Mol. Cell Biol. 2005; 6: 519-529Crossref PubMed Scopus (894) Google Scholar, 12Kawakami H. Keyamura K. Katayama T. J. Biol. Chem. 2005; 280: 27420-27430Abstract Full Text Full Text PDF PubMed Scopus (106) Google Scholar, 13Kawakami H. Ozaki S. Suzuki S. Nakamura K. Senriuchi T. Su'etsugu M. Fujimitsu K. Katayama T. Mol. Microbiol. 2006; 62: 1310-1324Crossref PubMed Scopus (32) Google Scholar, 14Nishida S. Fujimitsu K. Sekimizu K. Ohmura T. Ueda T. Katayama T. J. Biol. Chem. 2002; 277: 14986-14995Abstract Full Text Full Text PDF PubMed Scopus (107) Google Scholar). Erzberger et al. (9Erzberger J.P. Mott M.L. Berger J.M. Nat. Struct. Mol. Biol. 2006; 13: 676-683Crossref PubMed Scopus (236) Google Scholar) proposed an oligomeric structure for DnaA based on crystal structures of the ATP- and ADP-bound forms of DnaA domains III–IV from the hyperthermophilic bacterium Aquifex aeolicus. In this model of the initiation complex, the ATP-DnaA molecules assemble in a head-to-tail manner, and the resultant oligomers form a spiral helix, consistent with the known features of the AAA+ family proteins (11Hanson P.I. Whiteheart S.W. Nat. Rev. Mol. Cell Biol. 2005; 6: 519-529Crossref PubMed Scopus (894) Google Scholar, 15Indiani C. O'Donnell M. Nat. Rev. Mol. Cell Biol. 2006; 7: 751-761Crossref PubMed Scopus (145) Google Scholar). The structure-function relationships of the N-terminal domains I and II of DnaA remain obscure. The amino acid sequence of domain I (residues 1–86 in E. coli DnaA; Fig. 1A) is highly conserved among DnaA homologs of eubacterial species, that of domain II (residues in E. coli W. FEMS Microbiol. Rev. 2002; 26: 355-374PubMed Google Scholar). The structure of domain II is to a flexible of which is for DnaA function. Domain I in DnaA and DnaB helicase loading. A of domain I suggest that a region containing a crucial site for DnaA C. H. M. W. Mol. Microbiol. PubMed Scopus Google Scholar). The DnaA protein is inactive in for oriC and M.M. J.M. J. Biol. Chem. 2005; 280: Full Text Full Text PDF PubMed Scopus Google Scholar, M. J.M. Mol. Microbiol. 2003; PubMed Scopus Google Scholar). suggest that the to form oligomers is in this The of I interaction DnaA DnaB loading onto the region in the presence of DnaC H. N. K. J. Biol. Chem. Full Text PDF PubMed Google Scholar). of domain suggest that a region containing is for binding to DnaB the loading M. J.M. J. Biol. Chem. 1998; Full Text Full Text PDF PubMed Scopus Google the region containing is for with DnaB H. C. W. Mol. Microbiol. PubMed Scopus Google Scholar). The specific for DnaB loading remain to In DnaB loading is by that specifically to the domain III N terminus (residues J. J.M. J. Biol. Chem. Full Text PDF PubMed Google Scholar, J. W. T.R. C. S. J.M. J. Biol. Chem. Full Text Full Text PDF PubMed Scopus Google Scholar). DnaB interaction in domain I and domain II specific in the for DnaB loading M. J.M. J. Biol. Chem. 1998; Full Text Full Text PDF PubMed Scopus Google Scholar, H. C. W. Mol. Microbiol. PubMed Scopus Google Scholar). In the origin complex with the helicase J. 2005; PubMed Scopus Google that the interaction of an protein with a helicase is a conserved of the initiation the of the interaction and helicase loading remain to the structure of the DnaA N-terminal domain and the structure-function within this domain have to In the we determined the structure of the E. coli DnaA N terminus (residues 1–108) using NMR a that is crucial and specific for DnaB loading. we have that domain I weak affinity for carrying the AT-rich 13-mer within oriC for on we a model of DnaA formation and DnaB helicase in which a hydrophobic surface containing Trp-6 forms between the DnaA domain I within the DnaA Glu-21 for DnaB Protein of the DnaA N of the to amino acid by The DNA the and E. coli the of protein, the in containing and The DnaA N terminus (residues from E. coli by with and the in and on presence of and in The cell on and for The resultant A and and onto and The DnaA N terminus in the The proteins by using to on with A the The of the DnaA N terminus of of of flexible region the NMR for structural of protein Y. T. T. K. H. S. T. Cell. Full Text Full Text PDF PubMed Scopus Google Scholar). the DnaA N with for This the N terminus (residues which using This DnaA N terminus to on Protein in the by using in and and NMR and NMR on a NMR of the DnaA N terminus in and containing A of and and for the of the DnaA N the structural the of the of the and from the on a T. H. K. PubMed Scopus Google Scholar). The sequence used to the heteronuclear Overhauser by and S. J. Chem. Scopus Google Scholar). The NOE from the DnaA N terminus (residues 1–108) from and with a of S. J. J. NMR. 6: PubMed Scopus Google Scholar) used to the and to the The of the of amino acid using C. K. J. Mol. Biol. PubMed Scopus Google Scholar) used to the A of and on the of the and using J. NMR. 13: PubMed Scopus Google Scholar). The of the based on the of an The used for the structural in A of structures and the mean by the of the structures with the by the J.M. J. NMR. PubMed Scopus Google Scholar). using and M. K. J. Mol. PubMed Scopus Google Scholar). The domain I structure and poly(C)-binding protein using the II The used for the of NMR structures have in the The have in of structural for the DnaA N terminus from a of by and from a using the J.M. J. NMR. PubMed Scopus Google of and to to the mean structure for (residues for (residues of of of of of of of of of in the most in the in in the in a and the oriC 13-mer repeats and the and NMR the single quantum of protein in the presence of of to of the to The of the proteins and the for The changes to and of the DnaA proteins by a we H. Keyamura K. Katayama T. J. Biol. Chem. 2005; 280: 27420-27430Abstract Full Text Full Text PDF PubMed Scopus (106) Google Scholar, 13Kawakami H. Ozaki S. Suzuki S. Nakamura K. Senriuchi T. Su'etsugu M. Fujimitsu K. Katayama T. Mol. Microbiol. 2006; 62: 1310-1324Crossref PubMed Scopus (32) Google Scholar). The sequences of the used in The and of binding and replication using a and a with and we H. Keyamura K. Katayama T. J. Biol. Chem. 2005; 280: 27420-27430Abstract Full Text Full Text PDF PubMed Scopus (106) Google Scholar, 13Kawakami H. Ozaki S. Suzuki S. Nakamura K. Senriuchi T. Su'etsugu M. Fujimitsu K. Katayama T. Mol. Microbiol. 2006; 62: 1310-1324Crossref PubMed Scopus (32) Google Scholar, M. M. Kubota T. Y. Katayama T. PubMed Scopus Google Scholar). The form formation by et al. J. W. T.R. C. S. J.M. J. Biol. Chem. Full Text Full Text PDF PubMed Scopus Google Scholar) with DnaA for in containing of single protein of protein, of DnaB, of of DNA A of DNA and of The in the presence of and by A regulatory inactivation of DnaA used M. Shimuta T.R. Ishida T. Kawakami H. Katayama T. J. Biol. Chem. 2005; 280: 6528-6536Abstract Full Text Full Text PDF PubMed Scopus (82) Google Scholar, H. Su'etsugu M. Katayama T. J. Struct. Biol. 2006; PubMed Scopus Google that we used with the Su'etsugu and T. the for in of and containing of and form II The DNA-loaded using a with C. In the the of the DNA-loaded for in containing of the Hda, and to DnaA by by and by a The of the DnaA N the structure of the DnaA N terminus using NMR we amino acid with and the and The and we the and of the DnaA N terminus using a and heteronuclear NMR. to most in the DnaA N terminus for heteronuclear NOE based on the of the the in the domain I region (residues domain I to have a rigid structure in In the in a region a of the domain I terminus and domain II (residues that this region is flexible and we in the domain II region. we the DnaA N terminus distinct a rigid domain I and a domain the structure of the DnaA N terminus (residues 1–108) on the of a of that from and and that from using the J. NMR. 13: PubMed Scopus Google Scholar) A of structures and the structures and to The structures on the mean for the of of DnaA The from the mean for of These in The structure of the DnaA N terminus (residues 1–108) of (residues and and and a flexible terminus and The heteronuclear NOE consistent with the structure from and form an and and form a The is In a the from to that the from to the The hydrophobic of domain I consists of and Fig. These hydrophobic conserved in DnaA homologs in eubacterial Fig. that the of domain I is the C. J. Mol. Biol. PubMed Scopus Google Scholar) for proteins that similar to DnaA domain I (residues The K homology (KH) domain a that structure is similar to that of DnaA domain The KH domains have distinct motifs of I and the similar to Nucleic Acids Res. 2001; PubMed Scopus (217) Google Scholar). The the of DnaA domain I to of II KH domain, DnaA domain I has an α-α-β-β-α-β The of domain I is similar to that of the I KH domain that of the II KH domain of Domain KH domain is to form hydrophobic interaction S. H. J. Biol. Chem. 2005; 280: Full Text Full Text PDF PubMed Scopus Google Scholar). we on the hydrophobic interaction between DnaA domain I The hydrophobic interaction is that the changes of of domain I the to a the The of the DnaA N in the presence of changes of in the N-terminal and the between and and of and which on the surface and form a hydrophobic DnaA Trp-6 is crucial for weak interactions between DnaA molecules in M.M. J.M. J. Biol. Chem. 2005; 280: Full Text Full Text PDF PubMed Scopus Google Scholar, M. J.M. Mol. Microbiol. 2003; PubMed Scopus Google Scholar). the changes the that a of domain I forms a using the hydrophobic an interface Domain I a for the oriC for KH domain in nuclear K a protein and has in a of proteins K. Struct. Biol. 6: PubMed Scopus Google Scholar, H. Nucleic Acids Res. 21: PubMed Scopus Google Scholar). contains KH domains that specifically and with S. H. J. Biol. Chem. 2005; 280: Full Text Full Text PDF PubMed Scopus Google Scholar, J. Y. J. Biol. Chem. Full Text Full Text PDF PubMed Scopus Google Scholar). we used NMR to DnaA domain I with A the oriC 13-mer sequence changes in the of the DnaA N terminus (residues Fig. the to a the changes of we the to of the DNA These suggest that DnaA domain I has weak affinity for carrying the 13-mer the changes a of the of DnaA The changes of in the N-terminal of the and the between and a region Glu-21 and the oriC 13-mer ssDNA, changes and Fig. that the affinity of domain I for is with sequence and of DnaA Domain I on the structure and sequence homology of domain we within domain I to for a functional we and with using an H. Keyamura K. Katayama T. J. Biol. Chem. 2005; 280: 27420-27430Abstract Full Text Full Text PDF PubMed Scopus (106) Google Scholar, 13Kawakami H. Ozaki S. Suzuki S. Nakamura K. Senriuchi T. Su'etsugu M. Fujimitsu K. Katayama T. Mol. Microbiol. 2006; 62: 1310-1324Crossref PubMed Scopus (32) Google Scholar). These on the protein surface in Fig. and by we with the that highly conserved in DnaA of eubacterial Fig. and and with the of DnaA protein and H. Keyamura K. Katayama T. J. Biol. Chem. 2005; 280: 27420-27430Abstract Full Text Full Text PDF PubMed Scopus (106) Google Scholar, 13Kawakami H. Ozaki S. Suzuki S. Nakamura K. Senriuchi T. Su'etsugu M. Fujimitsu K. Katayama T. Mol. Microbiol. 2006; 62: 1310-1324Crossref PubMed Scopus (32) Google Scholar, T. N. T. M. Kubota T. Y. Sekimizu K. Katayama T. J. Biol. Chem. Full Text Full Text PDF PubMed Scopus Google Scholar). of the DnaA proteins of surface from a similar to the that the of DnaA and Fig. In of the proteins and Fig. of conserved most likely the structure of domain to of the of and located of the domain I structure Fig. with DnaA and proteins to in M.M. J.M. J. Biol. Chem. 2005; 280: Full Text Full Text PDF PubMed Scopus Google Scholar). The of and located of the structure determined in this Fig. the structure of DnaA in the in of the DnaA domain I we using which of the replication and replication of the chromosome. The of is form on for of the this the and the with we the of for and and the This is for the The the of formation that the of this protein in similar to that of the DnaA These that the initiation of DnaA is in In the initiation of DnaA and proteins in DnaA and proteins in in with the and for the on containing and The of for and the on of formation that of the the The that of the the in a of DnaA and of and and proteins and using a that we used for the DnaA and DnaA proteins H. Keyamura K. Katayama T. J. Biol. Chem. 2005; 280: 27420-27430Abstract Full Text Full Text PDF PubMed Scopus (106) Google Scholar, 13Kawakami H. Ozaki S. Suzuki S. Nakamura K. Senriuchi T. Su'etsugu M. Fujimitsu K. Katayama T. Mol. Microbiol. 2006; 62: 1310-1324Crossref PubMed Scopus (32) Google Scholar, 14Nishida S. Fujimitsu K. Sekimizu K. Ohmura T. Ueda T. Katayama T. J. Biol. Chem. 2002; 277: 14986-14995Abstract Full Text Full Text PDF PubMed Scopus (107) Google Scholar). The of the proteins Fig. In a DnaA proteins the affinity for ATP and the wild for and DnaA proteins for binding using a based on the of in a a replication with proteins J. Katayama T. EMBO J. 2001; 20: 4253-4262Crossref PubMed Scopus (217) Google Scholar, 12Kawakami H. Keyamura K. Katayama T. J. Biol. Chem. 2005; 280: 27420-27430Abstract Full Text Full Text PDF PubMed Scopus (106) Google Scholar, 13Kawakami H. Ozaki S. Suzuki S. Nakamura K. Senriuchi T. Su'etsugu M. Fujimitsu K. Katayama T. Mol. Microbiol. 2006; 62: 1310-1324Crossref PubMed Scopus (32) Google Scholar, M. M. Kubota T. Y. Katayama T. PubMed Scopus Google we the initiation of DnaA DnaA and initiation to that of the wild the of DnaA the protein with ATP to the replication the for replication a used for in DnaA proteins in the DnaA T.R. J.M. J. Biol. Chem. Full Text PDF PubMed Google Scholar, J.M. J. Biol. Chem. Full Text PDF PubMed Google Scholar). DnaA in the of Glu-21 in we open complex formation using the oriC and H. 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Microbiol. 2006; 62: 1310-1324Crossref PubMed Scopus (32) Google Scholar, H. N. K. J. Biol. Chem. Full Text PDF PubMed Google Scholar). The in this is with a structure a DnaA of replication on DnaB loading by DnaA to the in the presence of DnaA in replication and that this protein has a in DnaB loading. we DnaB helicase loading onto oriC. DnaB helicase is onto the open complex of oriC, by the helicase a specifically form form in the presence of DNA J. W. T.R. C. S. J.M. J. Biol. Chem. Full Text Full Text PDF PubMed Scopus Google Scholar, M.M. J.M. J. Biol. Chem. Full Text Full Text PDF PubMed Scopus Google Scholar). the DnaA to form and with the that the Glu-21 of DnaA a crucial in DnaB helicase loading. This is the to a DnaA domain I that is specifically for DnaB helicase loading. a that this for Glu-21 an we have that Glu-21 binds to DnaA in the which is to DnaA-ATP is with that is with the DNA-loaded form of the (3Katayama T. Kubota T. Kurokawa K. Crooke E. Sekimizu K. Cell. 1998; 94: 61-71Abstract Full Text Full Text PDF PubMed Scopus (263) Google Scholar, M. M. Kubota T. Y. Katayama T. PubMed Scopus Google Scholar). DnaA domain I is for this DnaA-ATP M. Shimuta T.R. Ishida T. Kawakami H. Katayama T. J. Biol. Chem. 2005; 280: 6528-6536Abstract Full Text Full Text PDF PubMed Scopus (82) Google Scholar). the for DnaA Glu-21 in this using a The DNA-loaded and with and The DnaA protein in DnaA-ATP a similar to the DnaA for DnaA and These the specific for Glu-21 in helicase loading. Domain I this we have the structure of DnaA domain DnaA domain I has structural to the KH structure and A crystal structure of the KH domain in revealed that forms S. H. J. Biol. Chem. 2005; 280: Full Text Full Text PDF PubMed Scopus Google Scholar) The hydrophobic which is of the and in PCBP2, to the dimerization. to the domain I has a hydrophobic that is by on structure and we have proposed a structural model of between domain I The domain I structure contains a hydrophobic surface within the N-terminal and the between and based on we suggest that this hydrophobic which an in DnaA This is consistent with that a DnaA protein to form M.M. J.M. J. Biol. Chem. 2005; 280: Full Text Full Text PDF PubMed Scopus Google Scholar, M. J.M. Mol. Microbiol. 2003; PubMed Scopus Google Scholar). A of the Trp-6 chain is of the domain I of is on the surface and Fig. This structure the of DnaA and in interactions between DnaA have that DnaA domain I form for the C-terminal domain of the is for and and a in which the C-terminal domain has by the DnaA domain I to have in C. H. M. W. Mol. Microbiol. PubMed Scopus Google Scholar). to the of the N-terminal amino to This is consistent with the model of the domain I structure in that located on the with that DnaA domain I Glu-21 a crucial and specific in DnaB helicase loading. DnaA the to form an open complex, that the interaction between DnaA molecules and DNA binding in this In DnaA has for loading DnaB onto DNA. of DnaA by and by functional using a M. J.M. J. Biol. Chem. 1998; Full Text Full Text PDF PubMed Scopus Google Scholar, H. C. W. Mol. Microbiol. PubMed Scopus Google Scholar, J. W. T.R. C. S. J.M. J. Biol. Chem. Full Text Full Text PDF PubMed Scopus Google Scholar). These the which the of the the we have a specifically for DnaB loading. on this and the domain I we suggest that the region Glu-21 and the N terminus of the is crucial for DnaB loading and This is consistent with analyses using forms of DnaA and DnaA and DnaB on for DnaA interactions and DnaB loading and located on opposite of domain I and This is in that the and interactions in the oriC initiation The DnaA complex by the DnaA protein is on oriC, which in of DnaB loading onto the open complex, DnaA is in DnaB loading onto in the M.M. J.M. J. Biol. Chem. Full Text Full Text PDF PubMed Scopus Google Scholar). formation of a DnaA on oriC is for DnaB loading onto the open complex. The is located in domain which most likely forms head-to-tail on oriC in AAA+ proteins (9Erzberger J.P. Mott M.L. Berger J.M. Nat. Struct. Mol. Biol. 2006; 13: 676-683Crossref PubMed Scopus (236) Google Scholar, 12Kawakami H. Keyamura K. Katayama T. J. Biol. Chem. 2005; 280: 27420-27430Abstract Full Text Full Text PDF PubMed Scopus (106) Google Scholar). suggest that domain I forms within the initiation complex the hydrophobic Trp-6 that domain I is by of domain I the domain II flexible which the DnaB interaction site of domain I on the surface of the initiation complex DnaB helicase is a and DnaB onto a single oriC open complex J.M. J. Biol. Chem. 2001; Full Text Full Text PDF PubMed Scopus Google Scholar, O'Donnell M. Mol. Cell. Full Text Full Text PDF PubMed Scopus (165) Google Scholar). The affinity of DnaA for DnaB is surface a of between the M. J.M. J. Biol. Chem. 1998; Full Text Full Text PDF PubMed Scopus Google Scholar). In on DnaA that with DnaB on the surface the domains which a to DnaB In the weak affinity of the domain I of DnaA molecules in the open complex the interaction between unwound oriC DNA and DnaB helicase by the single-stranded region in the of the DnaB site and DnaA on oriC for interaction with DnaB and for DnaB to with the region of unwound oriC. Trp-6 in E. coli DnaA is highly conserved among DnaA of Glu-21 is Fig. In to is conserved this The of and is this that for KH of nuclear K and within a single and repeats the binding affinity J.M. K. J. PubMed Scopus Google Scholar, M. Mol. Cell. 2001; 7: Full Text Full Text PDF PubMed Scopus Google Scholar). of DnaA the affinity of domain I for A of DnaA molecules in open complex this domain for interaction and to the of the DNA duplex is to with This is highly conserved among DnaA Fig. DnaA domain I has a rigid structure and is to domain III a flexible domain This structure that the of domain I is of the we that the weak affinity of domain I for is with the of the KH domains using NMR and structures have that with the of hydrophobic and S. H. J. Biol. Chem. 2005; 280: Full Text Full Text PDF PubMed Scopus Google Scholar, J. Y. J. Biol. Chem. Full Text Full Text PDF PubMed Scopus Google Scholar). with this the surface of domain I contains hydrophobic and The is a conserved in KH domains of This a in the forming a on the protein surface This and the of the of the for interactions with DNA and S. H. J. Biol. Chem. 2005; 280: Full Text Full Text PDF PubMed Scopus Google Scholar, K. Struct. Biol. 6: PubMed Scopus Google Scholar). The affinity of KH domains for DNA and is the A of the DnaA domain I is that the a the and and In the N-terminal of this and which the formation of the the of site within domain I is that that of KH which most likely the weak affinity of domain I for with