← Back to Search
Crystal Structure Of A Prokaryotic Replication Initiator Protein Bound To DNA At 2.6 Å Resolution
H. Komori, F. Matsunaga, Y. Higuchi, M. Ishiai, C. Wada, K. Miki
Published 1999 · Medicine, Biology
Download PDFAnalyze on Scholarcy
The initiator protein (RepE) of F factor, a plasmid involved in sexual conjugation in Escherichia coli, has dual functions during the initiation of DNA replication which are determined by whether it exists as a dimer or as a monomer. A RepE monomer functions as a replication initiator, but a RepE dimer functions as an autogenous repressor. We have solved the crystal structure of the RepE monomer bound to an iteron DNA sequence of the replication origin of plasmid F. The RepE monomer consists of topologically similar N‐ and C‐terminal domains related to each other by internal pseudo 2‐fold symmetry, despite the lack of amino acid similarities between the domains. Both domains bind to the two major grooves of the iteron (19 bp) with different binding affinities. The C‐terminal domain plays the leading role in this binding, while the N‐terminal domain has an additional role in RepE dimerization. The structure also suggests that superhelical DNA induced at the origin of plasmid F by four RepEs and one HU dimer has an essential role in the initiation of DNA replication.
This paper references
A program to produce both detailed and schematic plots of protein structures
P. Kraulis (1991)
Requirement of the Escherichia coli dnaA gene product for plasmid F maintenance.
B. Kline (1986)
Rapid purification of a cloned gene product by genetic fusion and site-specific proteolysis.
J. Germino (1984)
The localized melting of mini-F origin by the combined action of the mini-F initiator protein (RepE) and HU and DnaA of Escherichia coli
Y. Kawasaki (1996)
Requirement of the Escherichia coli dnaA gene function for ori-2-dependent mini-F plasmid replication.
Y. Murakami (1987)
Host participation in plasmid maintenance: dependence upon dnaA of replicons derived from P1 and F.
E. B. Hansen (1986)
The Hsp70 and Hsp60 chaperone
B. Bukau (1998)
Free R value: a novel statistical quantity for assessing the accuracy of crystal structures
A. Brünger (1992)
Binding of RepE initiator protein to mini-F DNA origin (ori2). Enhancing effects of repE mutations and DnaJ heat shock protein.
Y. Kawasaki (1992)
PROCHECK: a program to check the stereochemical quality of protein structures
R. Laskowski (1993)
Origin DNA-binding proteins.
A. Edwards (1998)
A leucine zipper motif determines different functions in a DNA replication protein.
D. García de Viedma (1996)
A 37 X 10(3) molecular weight plasmid-encoded protein is required for replication and copy number control in the plasmid pSC101 and its temperature-sensitive derivative pHS1.
K. Armstrong (1984)
NMRPipe: A multidimensional spectral processing system based on UNIX pipes
F. Delaglio (1995)
DNA-binding domain of the RepE initiator protein of mini-F plasmid: involvement of the carboxyl-terminal region.
F. Matsunaga (1995)
Free R value: a novel statistical quantity for assessing the accuracy of crystal structures.
A. T. Brunger (1992)
A 37ϫ10 3 molecular weight plasmid-encoded protein is required for replication and copy number control in the plasmid pSC101 and its temperaturesensitive derivative pFS1
K A Armstrong (1984)
Crystal Structure of the DNA-Binding Domain of the Epstein–Barr Virus Origin-Binding Protein, EBNA1, Bound to DNA
A. Bochkarev (1996)
X-ray diffraction data collection system for modern protein crystallography with a Weissenberg camera and an imaging plate using synchrotron radiation
N. Sakabe (1991)
The CCP4 suite: programs for protein crystallography.
Collaborative Computational (1994)
Genetic and functional analysis of the basic replicon of pPS10, a plasmid specific for Pseudomonas isolated from Pseudomonas syringae patovar savastanoi.
C. Nieto (1992)
Mechanism of autonomous control of the Escherichia coli F plasmid: different complexes of the initiator/repressor protein are bound to its operator and to an F plasmid replication origin.
L. Masson (1986)
The central region of RepE initiator protein of mini-F plasmid plays a crucial role in dimerization required for negative replication control.
F. Matsunaga (1997)
Crystallization of replication initiator protein (RepE54) of mini-F plasmid complexed with iteron DNA
H. Komori (1999)
Fundamental design of the high energy undulator pilot beamline for macromolecular crystallography at the SPring‐8
N. Kamiya (1995)
A review of mini-F plasmid maintenance.
B. Kline (1985)
A 37 103 molecular weight plasmid-encoded protein is required for replication and copy number control in the plasmid pSC101 and its temperaturesensitive derivative pFS1
K. A. Armstrong (1984)
Solution structure of the origin DNA-binding domain of SV40 T-antigen
X. Luo (1996)
Identification and characterization of a new replication region in the Neisseria gonorrhoeae beta-lactamase plasmid pFA3.
K. Gilbride (1990)
Crystallization and preliminary X-ray diffraction studies of a replication initiator protein (RepE54) of the mini-F plasmid complexed with iteron DNA.
H. Komori (1999)
X-ray diffraction data collection system for modern plate using synchrotron radiation
N Sakabe (1991)
Crystal structure at 1.7 Å of the bovine papillomavirus-1 E2 DMA-binding domain bound to its DNA target
R. Hegde (1992)
Processing of X-ray diffraction data collected in oscillation mode.
Z. Otwinowski (1997)
The TATA box binding protein.
S. Burley (1996)
Protein domains and conformational changes in the activation of RepA, a DNA replication initiator
R. Giraldo (1998)
Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees
S. Schultz (1991)
X-PLOR Version 3.1: A System for X-ray Crystallography and NMR
A. Brunger (1992)
Participation of hup gene product in ori2-dependent replication of fertility plasmid F.
M. Wada (1988)
Characterization of a replicon of the moderately promiscuous plasmid, pGSH5000, with features of both the mini‐replicon of pCU1 and the ori‐2 of F
Fernanda M. Silva‐Tatley (1993)
The helix-turn-helix DNA binding motif.
R. Brennan (1989)
Mutations within the replicon of the IncN plasmid pCU1 that affect its Escherichia coli polA-independence but not its autonomous replication ability.
B. Krishnan (1990)
MOLSCRIPT : a program package to produce both detailed and schematic plots of protein structures
P. R. Fobert (1991)
R. Giraldo (1989)
The Hsp70 and Hsp60 Chaperone Machines
B. Bukau (1998)
Origin DNAbinding proteins
A. M. Edwards (1998)
The winged-helix DNA-binding motif: Another helix-turn-helix takeoff
R. Brennan (1993)
Replication initiator protein RepE of mini-F plasmid: functional differentiation between monomers (initiator) and dimers (autogenous repressor).
M. Ishiai (1994)
DNA-binding domain of the RepE initiator protein of mini-F plasmid: involvement of the C-terminal region
F. Matsunaga (1995)
A model for initiation at origins of DNA replication
D. Bramhill (1988)
3-Å resolution structure of a protein with histone-like properties in prokaryotes
I. Tanaka (1984)
Crystal structure of TFIID TATA-box binding protein
D. Nikolov (1992)
Replication and Control of Circular Bacterial Plasmids
G. del Solar (1998)
Nine unique repeating sequences in a region essential for replication and incompatibility of the mini-F plasmid.
T. Murotsu (1981)
Raster3D Version 2.0. A program for photorealistic molecular graphics.
E. Merritt (1994)
T A Jones (1994)
Genetic and functional analysis of the basic replicon of pPS10, a plasmid specific for Pseudomonas isolated from Pseudomonas syringae pathovar savastanoi
C. Nieto (1992)
This paper is referenced by
Structure-based functional analysis of the replication protein of plasmid R6K: key amino acids at the pi/DNA interface.
S. Kunnimalaiyaan (2007)
Origin pairing (‘handcuffing’) and unpairing in the control of P1 plasmid replication
N. Das (2004)
Historical Events That Spawned the Field of Plasmid Biology.
C. Kado (2014)
Common domains in the initiators of DNA replication in Bacteria, Archaea and Eukarya: combined structural, functional and phylogenetic perspectives.
R. Giraldo (2003)
E2F-7: a distinctive E2F family member with an unusual organization of DNA-binding domains
N. Logan (2004)
Reconstitution of F Factor DNA Replication in Vitro with Purified Proteins*
S. Zzaman (2004)
Voyage of RepA protein from plasmid DNA replication through amyloid aggregation towards synthetic biology
R. Giraldo (2010)
Conformation of a plasmid replication initiator protein affects its proteolysis by ClpXP system
M. Pierechod (2009)
Structural basis for regulation of bifunctional roles in replication initiator protein
A. Nakamura (2007)
Structural Basis for Replication Origin Unwinding by an Initiator Primase of Plasmid ColE2-P9
H. Itou (2014)
Replication and partitioning of the broad-host-range plasmid RK2.
Katarzyna Kolatka (2010)
Fluorescence studies of the replication initiator protein RepA in complex with operator and iteron sequences and free in solution
R. E. Diederix (2008)
Tandem DNA recognition by PhoB, a two-component signal transduction transcriptional activator.
A. Blanco (2002)
Conserved hydrophobic amino acid residues in the N-terminal region of DnaA protein are involved in DnaA-DnaA interaction.
S. Mima (2002)
Extrachromosomal element capture and the evolution of multiple replication origins in archaeal chromosomes
N. Robinson (2007)
Role of π Dimers in Coupling (“Handcuffing”) of Plasmid R6K's γ ori Iterons
S. Kunnimalaiyaan (2005)
Specific interaction between the initiator protein (Rep) and origin of plasmid ColE2-P9.
M. Han (2007)
Similarities between the DNA replication initiators of Gram-negative bacteria plasmids (RepA) and eukaryotes (Orc4p)/archaea (Cdc6p)
R. Giraldo (2001)
Strategies for helicase recruitment and loading in bacteria
I. Konieczny (2003)
π Protein‐ and ATP‐dependent transitions from ‘closed’ to ‘open’ complexes at the γ ori of plasmid R6K
R. Krüger (2003)
Dimers of pi protein bind the A+T-rich region of the R6K gamma origin near the leading-strand synthesis start sites: regulatory implications.
R. Krüger (2000)
Plasmids of the Genus Pseudomonas
Christopher M Thomas (2004)
Structural analysis of a replication protein encoded by a plasmid isolated from a multiple sclerosis patient
T. Kilic (2019)
Mechanisms of Plasmid Replication
N. Khan (2017)
Plasmid R6K replication control.
Sheryl A. Rakowski (2013)
Label-Free, Multiplexed, Single-Molecule Analysis of Protein-DNA Complexes with Nanopores.
Garbiñe Celaya (2017)
Modulation of pPS10 host range by plasmid-encoded RepA initiator protein.
B. Maestro (2003)
Replisome Assembly at Bacterial Chromosomes and Iteron Plasmids
K. Węgrzyn (2016)
Organization, Replication, Transposition, and Repair of DNA
David E. Metzler (2001)
Stn1-Ten1 is an Rpa2-Rpa3-like complex at telomeres.
J. Sun (2009)
The Rep20 Replication Initiator From the pAG20 Plasmid of Acetobacter aceti
M. Babič (2013)
Recruitment of Hsp70 chaperones: a crucial part of viral survival strategies.
M. Mayer (2005)See more