1J9I

STRUCTURE OF THE DNA BINDING DOMAIN OF THE GPNU1 SUBUNIT OF LAMBDA TERMINASE

• PDB DOI: https://doi.org/10.2210/pdb1J9I/pdb
• BMRB: 4752

• Classification: VIRAL PROTEIN
• Organism(s): Lambdavirus lambda
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-05-25 Released: 2002-08-14 
• Deposition Author(s): De Beer, T., Meyer, J., Ortega, M., Yang, Q., Maes, L., Duffy, C., Berton, N., Sippy, J., Overduin, M., Feiss, M., Catalano, C.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Insights into specific DNA recognition during the assembly of a viral genome packaging machine.

de Beer, T., Fang, J., Ortega, M., Yang, Q., Maes, L., Duffy, C., Berton, N., Sippy, J., Overduin, M., Feiss, M., Catalano, C.E.

(2002) Mol Cell 9: 981-991

• PubMed: 12049735 
• DOI: https://doi.org/10.1016/s1097-2765(02)00537-3
• Primary Citation of Related Structures:  
  1J9I


• PubMed Abstract: 
  

  Terminase enzymes mediate genome "packaging" during the reproduction of DNA viruses. In lambda, the gpNu1 subunit guides site-specific assembly of terminase onto DNA. The structure of the dimeric DNA binding domain of gpNu1 was solved using nuclear magnetic resonance spectroscopy. Its fold contains a unique winged helix-turn-helix (wHTH) motif within a novel scaffold. Surprisingly, a predicted P loop ATP binding motif is in fact the wing of the DNA binding motif. Structural and genetic analysis has identified determinants of DNA recognition specificity within the wHTH motif and the DNA recognition sequence. The structure reveals an unexpected DNA binding mode and provides a mechanistic basis for the concerted action of gpNu1 and Escherichia coli integration host factor during assembly of the packaging machinery.

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Organizational Affiliation: 

Department of Pharmacology, University of Colorado Health Sciences Center, Denver 80262, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 15.64 kDa 
• Atom Count: 1,098 
• Modelled Residue Count: 136 
• Deposited Residue Count: 136 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TERMINASE SMALL SUBUNIT	A, B	68	Lambdavirus lambda	Mutation(s): 0  Gene Names: NU1
UniProt
Find proteins for P03707 (Escherichia phage lambda) Explore P03707  Go to UniProtKB:  P03707

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-08-14 
Deposition Author(s): De Beer, T., Meyer, J., Ortega, M., Yang, Q., Maes, L., Duffy, C., Berton, N., Sippy, J., Overduin, M., Feiss, M., Catalano, C.

Revision History  

• Version 1.0: 2002-08-14
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-23
  Changes: Data collection, Database references, Derived calculations