1LRR | pdb_00001lrr

CRYSTAL STRUCTURE OF E. COLI SEQA COMPLEXED WITH HEMIMETHYLATED DNA

• PDB DOI: https://doi.org/10.2210/pdb1LRR/pdb
• NAKB: 1LRR

• Classification: REPLICATION INHIBITOR/DNA
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-05-15 Released: 2002-12-11 
• Deposition Author(s): Guarne, A., Zhao, Q., Guirlando, R., Yang, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.278 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.248 (Depositor), 0.249 (DCC) 

Starting Model: experimental

Literature

Insights into negative modulation of E. coli replication initiation from the structure of SeqA-hemimethylated DNA complex

Guarne, A., Zhao, Q., Guirlando, R., Yang, W.

(2002) Nat Struct Biol 9: 839-843

• PubMed: 12379844 
• DOI: https://doi.org/10.1038/nsb857
• Primary Citation Related Structures: 
  1LRR


• PubMed Abstract: 
  

  The SeqA protein binds clusters of fully methylated or hemimethylated GATC sequences at oriC and negatively modulates the initiation of DNA replication. We find that SeqA can be proteolytically cleaved into an N-terminal multimerization and a C-terminal DNA-binding domain and have determined the crystal structure of the C-terminal domain in complex with a hemimethylated GATC site. SeqA makes direct hydrogen bonds and van der Waals contacts with the hemimethylated A-T base pair in addition to interactions with the surrounding bases and DNA backbone. The tetrameric protein-DNA complex found in the crystal suggests that SeqA binds multiple GATC sites on separate DNA duplexes, altering the overall DNA topology and sequestering oriC from replication initiation.

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Organizational Affiliation: 
• Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 44.2 kDa 
• Atom Count: 2,895 
• Modeled Residue Count: 284 
• Deposited Residue Count: 310 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SeqA protein	E [auth A], F [auth D]	131	Escherichia coli	Mutation(s): 0  Gene Names: seqA
UniProt
Find proteins for P0AFY8 (Escherichia coli (strain K12)) Explore P0AFY8  Go to UniProtKB:  P0AFY8

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*CP*AP*CP*CP*GP*AP*TP*CP*GP*AP*CP*T)-3'	A [auth B], C [auth E]	12	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*AP*GP*TP*CP*GP*(6MA)P*TP*CP*GP*GP*TP*G)-3'	B [auth C], D [auth F]	12	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.278 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.248 (Depositor), 0.249 (DCC) 

Space Group: P 4₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.493	α = 90
b = 106.493	β = 90
c = 49.078	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-12-11 
Deposition Author(s): Guarne, A., Zhao, Q., Guirlando, R., Yang, W.

Revision History  

• Version 1.0: 2002-12-11
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2013-05-29
  Changes: Atomic model
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2024-04-03
  Changes: Refinement description