1J3E

Crystal Structure of the E.coli SeqA protein complexed with N6-methyladenine- guanine mismatch DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Structural and biochemical analyses of hemimethylated DNA binding by the SeqA protein

Fujikawa, N., Kurumizaka, H., Nureki, O., Tanaka, Y., Yamazoe, M., Hiraga, S., Yokoyama, S.

(2004) Nucleic Acids Res. 32: 82-92

  • DOI: 10.1093/nar/gkh173
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The Escherichia coli SeqA protein recognizes the 11 hemimethylated G-mA-T-C sites in the oriC region of the chromosome, and prevents replication over-initiation within one cell cycle. The crystal structure of the SeqA C-terminal domain with hemimethy ...

    The Escherichia coli SeqA protein recognizes the 11 hemimethylated G-mA-T-C sites in the oriC region of the chromosome, and prevents replication over-initiation within one cell cycle. The crystal structure of the SeqA C-terminal domain with hemimethylated DNA revealed the N6-methyladenine recognition mechanism; however, the mechanism of discrimination between the hemimethylated and fully methylated states has remained elusive. In the present study, we performed mutational analyses of hemimethylated G-mA-T-C sequences with the minimal DNA-binding domain of SeqA (SeqA71-181), and found that SeqA71-181 specifically binds to hemimethylated DNA containing a sequence with a mismatched mA:G base pair [G-mA(:G)-T-C] as efficiently as the normal hemimethylated G-mA(:T)-T-C sequence. We determined the crystal structures of SeqA71-181 complexed with the mismatched and normal hemimethylated DNAs at 2.5 and 3.0 A resolutions, respectively, and found that the mismatched mA:G base pair and the normal mA:T base pair are recognized by SeqA in a similar manner. Furthermore, in both crystal structures, an electron density is present near the unmethylated adenine, which is only methylated in the fully methylated state. This electron density, which may be due to a water molecule or a metal ion, can exist in the hemimethylated state, but not in the fully methylated state, because of steric clash with the additional methyl group.

    Organizational Affiliation: 

    RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.




Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
SeqA protein
A
115Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: seqA
Find proteins for P0AFY8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AFY8
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*AP*AP*GP*GP*(6MA)P*TP*CP*CP*AP*A)-3'B10N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*TP*TP*GP*GP*AP*GP*CP*CP*TP*T)-3'C10N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
6MA
Query on 6MA
B
DNA LINKINGC11 H16 N5 O6 PA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.230 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 33.432α = 90.00
b = 65.061β = 90.00
c = 77.176γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
DENZOdata reduction
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-05-18
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance