PDBsum entry 1j1v

Replication/DNA

PDB id

1j1v

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Contents

			Protein chain

					94 a.a. *

			DNA/RNA

			Waters ×143

* Residue conservation analysis

PDB id:

1j1v

Links

Name:

Replication/DNA

Title:

Crystal structure of dnaa domainiv complexed with dnaabox DNA

Structure:

5'-d( Tp Gp Tp Tp Ap Tp Cp Cp Ap Cp Ap Gp G)-3'. Chain: b. Synonym: dnaabox DNA. Engineered: yes. 5'-d( Cp Cp Tp Gp Tp Gp Gp Ap Tp Ap Ap Cp A)-3'. Chain: c. Synonym: dnaabox DNA. Engineered: yes. Chromosomal replication initiator protein dnaa.

Source:

Synthetic: yes. Escherichia coli. Organism_taxid: 562. Gene: dnaa. Other_details: cell-free protein synthesis system

Biol. unit:

Trimer (from PQS)

Resolution:

2.10Å

R-factor:

0.229

R-free:

0.249

Authors:

N.Fujikawa,H.Kurumizaka,O.Nureki,T.Terada,M.Shirouzu,T.Katayama, S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

N.Fujikawa et al. (2003). Structural basis of replication origin recognition by the DnaA protein. Nucleic Acids Res, 31, 2077-2086. PubMed id: 12682358 DOI: 10.1093/nar/gkg309

Date:

18-Dec-02

Release date:

22-Apr-03

PROCHECK

	Headers

	References

Protein chain

P03004 (DNAA_ECOLI) - Chromosomal replication initiator protein DnaA from Escherichia coli (strain K12)

Seq: Struc:					467 a.a. 94 a.a.

Key:

PfamA domain

Secondary structure

CATH domain

DNA/RNA chains

		T-G-T-T-A-T-C-C-A-C-A-G-G 13 bases
		C-C-T-G-T-G-G-A-T-A-A-C-A 13 bases

DOI no: 10.1093/nar/gkg309	Nucleic Acids Res 31:2077-2086 (2003)
PubMed id: 12682358

Structural basis of replication origin recognition by the DnaA protein.
N.Fujikawa, H.Kurumizaka, O.Nureki, T.Terada, M.Shirouzu, T.Katayama, S.Yokoyama.

ABSTRACT

Escherichia coli DnaA binds to 9 bp sequences (DnaA boxes) in the replication origin, oriC, to form a complex initiating chromosomal DNA replication. In the present study, we determined the crystal structure of its DNA-binding domain (domain IV) complexed with a DnaA box at 2.1 A resolution. DnaA domain IV contains a helix-turn-helix motif for DNA binding. One helix and a loop of the helix- turn-helix motif are inserted into the major groove and 5 bp (3' two-thirds of the DnaA box sequence) are recognized through base-specific hydrogen bonds and van der Waals contacts with the C5-methyl groups of thymines. In the minor groove, Arg399, located in the loop adjacent to the motif, recognizes three more base pairs (5' one-third of the DnaA box sequence) by base-specific hydrogen bonds. DNA bending by approximately 28 degrees was also observed in the complex. These base-specific interactions explain how DnaA exhibits higher affinity for the strong DnaA boxes (R1, R2 and R4) than the weak DnaA boxes (R3 and M) in the replication origin.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21227921

E.C.Dueber, A.Costa, J.E.Corn, S.D.Bell, and J.M.Berger (2011).
Molecular determinants of origin discrimination by Orc1 initiators in archaea.

Nucleic Acids Res, 39, 3621-3631.

21035377

A.C.Leonard, and J.E.Grimwade (2010).
Regulating DnaA complex assembly: it is time to fill the gaps.

Curr Opin Microbiol, 13, 766-772.

20130679

H.Kawakami, and T.Katayama (2010).
DnaA, ORC, and Cdc6: similarity beyond the domains of life and diversity.

Biochem Cell Biol, 88, 49-62.

20157337

T.Katayama, S.Ozaki, K.Keyamura, and K.Fujimitsu (2010).
Regulation of the replication cycle: conserved and diverse regulatory systems for DnaA and oriC.

Nat Rev Microbiol, 8, 163-170.

19940251

G.Natrajan, M.F.Noirot-Gros, A.Zawilak-Pawlik, U.Kapp, and L.Terradot (2009).
The structure of a DnaA/HobA complex from Helicobacter pylori provides insight into regulation of DNA replication in bacteria.

Proc Natl Acad Sci U S A, 106, 21115-21120.

PDB code:

2wp0

19400775

K.Boeneman, S.Fossum, Y.Yang, N.Fingland, K.Skarstad, and E.Crooke (2009).
Escherichia coli DnaA forms helical structures along the longitudinal cell axis distinct from MreB filaments.

Mol Microbiol, 72, 645-657.

19401329

K.Fujimitsu, T.Senriuchi, and T.Katayama (2009).
Specific genomic sequences of E. coli promote replicational initiation by directly reactivating ADP-DnaA.

Genes Dev, 23, 1221-1233.

19632993

K.Keyamura, Y.Abe, M.Higashi, T.Ueda, and T.Katayama (2009).
DiaA dynamics are coupled with changes in initial origin complexes leading to helicase loading.

J Biol Chem, 284, 25038-25050.

19000695

Q.Xu, D.McMullan, P.Abdubek, T.Astakhova, D.Carlton, C.Chen, H.J.Chiu, T.Clayton, D.Das, M.C.Deller, L.Duan, M.A.Elsliger, J.Feuerhelm, J.Hale, G.W.Han, L.Jaroszewski, K.K.Jin, H.A.Johnson, H.E.Klock, M.W.Knuth, P.Kozbial, S.Sri Krishna, A.Kumar, D.Marciano, M.D.Miller, A.T.Morse, E.Nigoghossian, A.Nopakun, L.Okach, S.Oommachen, J.Paulsen, C.Puckett, R.Reyes, C.L.Rife, N.Sefcovic, C.Trame, H.van den Bedem, D.Weekes, K.O.Hodgson, J.Wooley, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2009).
A structural basis for the regulatory inactivation of DnaA.

J Mol Biol, 385, 368-380.

PDB code:

3bos

18704949

S.Biswas, M.Guharoy, and P.Chakrabarti (2009).
Dissection, residue conservation, and structural classification of protein-DNA interfaces.

Proteins, 74, 643-654.

18466918

I.Lozada-Chávez, V.E.Angarica, J.Collado-Vides, and B.Contreras-Moreira (2008).
The role of DNA-binding specificity in the evolution of bacterial regulatory networks.

J Mol Biol, 379, 627-643.

18660512

N.V.Sernova, and M.S.Gelfand (2008).
Identification of replication origins in prokaryotic genomes.

Brief Bioinform, 9, 376-391.

18312360

S.Fossum, G.De Pascale, C.Weigel, W.Messer, S.Donadio, and K.Skarstad (2008).
A robust screen for novel antibiotics: specific knockout of the initiator of bacterial DNA replication.

FEMS Microbiol Lett, 281, 210-214.

18957591

S.Nozaki, and T.Ogawa (2008).
Determination of the minimum domain II size of Escherichia coli DnaA protein essential for cell viability.

Microbiology, 154, 3379-3384.

18922190

V.E.Angarica, A.G.Pérez, A.T.Vasconcelos, J.Collado-Vides, and B.Contreras-Moreira (2008).
Prediction of TF target sites based on atomistic models of protein-DNA complexes.

BMC Bioinformatics, 9, 436.

17761879

E.L.Dueber, J.E.Corn, S.D.Bell, and J.M.Berger (2007).
Replication origin recognition and deformation by a heterodimeric archaeal Orc1 complex.

Science, 317, 1210-1213.

PDB code:

2qby

17683397

G.Natrajan, D.R.Hall, A.C.Thompson, I.Gutsche, and L.Terradot (2007).
Structural similarity between the DnaA-binding proteins HobA (HP1230) from Helicobacter pylori and DiaA from Escherichia coli.

Mol Microbiol, 65, 995.

PDB code:

2uvp

17699754

K.Keyamura, N.Fujikawa, T.Ishida, S.Ozaki, M.Su'etsugu, K.Fujimitsu, W.Kagawa, S.Yokoyama, H.Kurumizaka, and T.Katayama (2007).
The interaction of DiaA and DnaA regulates the replication cycle in E. coli by directly promoting ATP DnaA-specific initiation complexes.

Genes Dev, 21, 2083-2099.

PDB code:

2yva

17435790

M.L.Mott, and J.M.Berger (2007).
DNA replication initiation: mechanisms and regulation in bacteria.

Nat Rev Microbiol, 5, 343-354.

17932079

S.Ishikawa, Y.Ogura, M.Yoshimura, H.Okumura, E.Cho, Y.Kawai, K.Kurokawa, T.Oshima, and N.Ogasawara (2007).
Distribution of stable DnaA-binding sites on the Bacillus subtilis genome detected using a modified ChIP-chip method.

DNA Res, 14, 155-168.

17680349

T.J.Lowery, J.G.Pelton, J.M.Chandonia, R.Kim, H.Yokota, and D.E.Wemmer (2007).
NMR structure of the N-terminal domain of the replication initiator protein DnaA.

J Struct Funct Genomics, 8, 11-17.

PDB code:

2jmp

16594962

C.Weigel, and H.Seitz (2006).
Bacteriophage replication modules.

FEMS Microbiol Rev, 30, 321-381.

17042785

H.Kawakami, S.Ozaki, S.Suzuki, K.Nakamura, T.Senriuchi, M.Su'etsugu, K.Fujimitsu, and T.Katayama (2006).
The exceptionally tight affinity of DnaA for ATP/ADP requires a unique aspartic acid residue in the AAA+ sensor 1 motif.

Mol Microbiol, 62, 1310-1324.

16829961

J.P.Erzberger, M.L.Mott, and J.M.Berger (2006).
Structural basis for ATP-dependent DnaA assembly and replication-origin remodeling.

Nat Struct Mol Biol, 13, 676-683.

PDB code:

2hcb

16611245

S.Ozaki, K.Fujimitsu, H.Kurumizaka, and T.Katayama (2006).
The DnaA homolog of the hyperthermophilic eubacterium Thermotoga maritima forms an open complex with a minimal 149-bp origin region in an ATP-dependent manner.

Genes Cells, 11, 425-438.

15808743

L.Aravind, V.Anantharaman, S.Balaji, M.M.Babu, and L.M.Iyer (2005).
The many faces of the helix-turn-helix domain: transcription regulation and beyond.

FEMS Microbiol Rev, 29, 231-262.

15995226

V.Gabrovsky, M.L.Yamamoto, and J.H.Miller (2005).
Mutator effects in Escherichia coli caused by the expression of specific foreign genes.

J Bacteriol, 187, 5044-5048.

15634350

Y.Tanaka, H.Kurumizaka, and S.Yokoyama (2005).
CpG methylation of the CENP-B box reduces human CENP-B binding.

FEBS J, 272, 282-289.

14978287

K.C.McGarry, V.T.Ryan, J.E.Grimwade, and A.C.Leonard (2004).
Two discriminatory binding sites in the Escherichia coli replication origin are required for DNA strand opening by initiator DnaA-ATP.

Proc Natl Acad Sci U S A, 101, 2811-2816.

15189445

M.Su'etsugu, M.Takata, T.Kubota, Y.Matsuda, and T.Katayama (2004).
Molecular mechanism of DNA replication-coupled inactivation of the initiator protein in Escherichia coli: interaction of DnaA with the sliding clamp-loaded DNA and the sliding clamp-Hda complex.

Genes Cells, 9, 509-522.

15358831

S.A.Capaldi, and J.M.Berger (2004).
Biochemical characterization of Cdc6/Orc1 binding to the replication origin of the euryarchaeon Methanothermobacter thermoautotrophicus.

Nucleic Acids Res, 32, 4821-4832.

15569148

T.R.Shimuta, K.Nakano, Y.Yamaguchi, S.Ozaki, K.Fujimitsu, C.Matsunaga, K.Noguchi, A.Emoto, and T.Katayama (2004).
Novel heat shock protein HspQ stimulates the degradation of mutant DnaA protein in Escherichia coli.

Genes Cells, 9, 1151-1166.

12940821

M.Su'etsugu, A.Emoto, K.Fujimitsu, K.Keyamura, and T.Katayama (2003).
Transcriptional control for initiation of chromosomal replication in Escherichia coli: fluctuation of the level of origin transcription ensures timely initiation.

Genes Cells, 8, 731-745.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.