Structure for the N-terminus of chromosomal replication initiation protein dnaA from M. genitalium

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report

This is version 1.6 of the entry. See complete history


NMR structure of the N-terminal domain of the replication initiator protein DnaA.

Lowery, T.J.Pelton, J.G.Chandonia, J.M.Kim, R.Yokota, H.Wemmer, D.E.

(2007) J Struct Funct Genomics 8: 11-17

  • DOI: https://doi.org/10.1007/s10969-007-9022-7
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    DnaA is an essential component in the initiation of bacterial chromosomal replication. DnaA binds to a series of 9 base pair repeats leading to oligomerization, recruitment of the DnaBC helicase, and the assembly of the replication fork machinery. The structure of the N-terminal domain (residues 1-100) of DnaA from Mycoplasma genitalium was determined by NMR spectroscopy. The backbone r.m.s.d. for the first 86 residues was 0.6 +/- 0.2 A based on 742 NOE, 50 hydrogen bond, 46 backbone angle, and 88 residual dipolar coupling restraints. Ultracentrifugation studies revealed that the domain is monomeric in solution. Features on the protein surface include a hydrophobic cleft flanked by several negative residues on one side, and positive residues on the other. A negatively charged ridge is present on the opposite face of the protein. These surfaces may be important sites of interaction with other proteins involved in the replication process. Together, the structure and NMR assignments should facilitate the design of new experiments to probe the protein-protein interactions essential for the initiation of DNA replication.

  • Organizational Affiliation

    Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chromosomal replication initiator protein dnaA107Mycoplasmoides genitaliumMutation(s): 0 
Gene Names: dnaA
Find proteins for P35888 (Mycoplasma genitalium (strain ATCC 33530 / DSM 19775 / NCTC 10195 / G37))
Explore P35888 
Go to UniProtKB:  P35888
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35888
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-07-17
    Type: Initial release
  • Version 1.1: 2007-12-18
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-02-05
    Changes: Data collection, Database references, Derived calculations, Other
  • Version 1.4: 2023-06-14
    Changes: Database references, Other
  • Version 1.5: 2023-12-20
    Changes: Data collection, Other
  • Version 1.6: 2024-05-08
    Changes: Database references