title: A structural basis for the regulatory inactivation of DnaA.
abstract: Regulatory inactivation of DnaA is dependent on Hda (homologous to DnaA), a protein homologous to the AAA+ (ATPases associated with diverse cellular activities) ATPase region of the replication initiator DnaA. When bound to the sliding clamp loaded onto duplex DNA, Hda can stimulate the transformation of active DnaA-ATP into inactive DnaA-ADP. The crystal structure of Hda from Shewanella amazonensis SB2B at 1.75 A resolution reveals that Hda resembles typical AAA+ ATPases. The arrangement of the two subdomains in Hda (residues 1-174 and 175-241) differs dramatically from that of DnaA. A CDP molecule anchors the Hda domains in a conformation that promotes dimer formation. The Hda dimer adopts a novel oligomeric assembly for AAA+ proteins in which the arginine finger, crucial for ATP hydrolysis, is fully exposed and available to hydrolyze DnaA-ATP through a typical AAA+ type of mechanism. The sliding clamp binding motifs at the N-terminus of each Hda monomer are partially buried and combine to form an antiparallel beta-sheet at the dimer interface. The inaccessibility of the clamp binding motifs in the CDP-bound structure of Hda suggests that conformational changes are required for Hda to form a functional complex with the clamp. Thus, the CDP-bound Hda dimer likely represents an inactive form of Hda.
authors.affiliation: Stanford Synchrotron Radiation Lightsource, Stanford University, Menlo Park, CA, USA.
authors.forename: Qingping
authors.initials: Q
authors.lastname: Xu
authors.forename: Daniel
authors.initials: D
authors.lastname: McMullan
authors.forename: Polat
authors.initials: P
authors.lastname: Abdubek
authors.forename: Tamara
authors.initials: T
authors.lastname: Astakhova
authors.forename: Dennis
authors.initials: D
authors.lastname: Carlton
authors.forename: Connie
authors.initials: C
authors.lastname: Chen
authors.forename: Hsiu-Ju
authors.initials: HJ
authors.lastname: Chiu
authors.forename: Thomas
authors.initials: T
authors.lastname: Clayton
authors.forename: Debanu
authors.initials: D
authors.lastname: Das
authors.forename: Marc C
authors.initials: MC
authors.lastname: Deller
authors.forename: Lian
authors.initials: L
authors.lastname: Duan
authors.forename: Marc-Andre
authors.initials: MA
authors.lastname: Elsliger
authors.forename: Julie
authors.initials: J
authors.lastname: Feuerhelm
authors.forename: Joanna
authors.initials: J
authors.lastname: Hale
authors.forename: Gye Won
authors.initials: GW
authors.lastname: Han
authors.forename: Lukasz
authors.initials: L
authors.lastname: Jaroszewski
authors.forename: Kevin K
authors.initials: KK
authors.lastname: Jin
authors.forename: Hope A
authors.initials: HA
authors.lastname: Johnson
authors.forename: Heath E
authors.initials: HE
authors.lastname: Klock
authors.forename: Mark W
authors.initials: MW
authors.lastname: Knuth
authors.forename: Piotr
authors.initials: P
authors.lastname: Kozbial
authors.forename: S
authors.initials: S
authors.lastname: Sri Krishna
authors.forename: Abhinav
authors.initials: A
authors.lastname: Kumar
authors.forename: David
authors.initials: D
authors.lastname: Marciano
authors.forename: Mitchell D
authors.initials: MD
authors.lastname: Miller
authors.forename: Andrew T
authors.initials: AT
authors.lastname: Morse
authors.forename: Edward
authors.initials: E
authors.lastname: Nigoghossian
authors.forename: Amanda
authors.initials: A
authors.lastname: Nopakun
authors.forename: Linda
authors.initials: L
authors.lastname: Okach
authors.forename: Silvya
authors.initials: S
authors.lastname: Oommachen
authors.forename: Jessica
authors.initials: J
authors.lastname: Paulsen
authors.forename: Christina
authors.initials: C
authors.lastname: Puckett
authors.forename: Ron
authors.initials: R
authors.lastname: Reyes
authors.forename: Christopher L
authors.initials: CL
authors.lastname: Rife
authors.forename: Natasha
authors.initials: N
authors.lastname: Sefcovic
authors.forename: Christine
authors.initials: C
authors.lastname: Trame
authors.forename: Henry
authors.initials: H
authors.lastname: van den Bedem
authors.forename: Dana
authors.initials: D
authors.lastname: Weekes
authors.forename: Keith O
authors.initials: KO
authors.lastname: Hodgson
authors.forename: John
authors.initials: J
authors.lastname: Wooley
authors.forename: Ashley M
authors.initials: AM
authors.lastname: Deacon
authors.forename: Adam
authors.initials: A
authors.lastname: Godzik
authors.forename: Scott A
authors.initials: SA
authors.lastname: Lesley
authors.forename: Ian A
authors.initials: IA
authors.lastname: Wilson
mesh_terms: D000251:Adenosine Triphosphatases / Q000737:chemistry*; D000255:Adenosine Triphosphate / Q000378:metabolism; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000378:metabolism*; D018360:Crystallography, X-Ray; D004268:DNA-Binding Proteins / Q000378:metabolism*; D019281:Dimerization; D008958:Models, Molecular; D008969:Molecular Sequence Data; D020836:Protein Structure, Quaternary; D016415:Sequence Alignment; D020592:Shewanella / Q000201:enzymology
chemical_list: D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; C066312:DnaA protein, Bacteria; D000255:Adenosine Triphosphate; D000251:Adenosine Triphosphatases