2OWO | pdb_00002owo

Last Stop on the Road to Repair: Structure of E.coli DNA Ligase Bound to Nicked DNA-Adenylate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.254 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.222 (DCC) 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 

Literature

Last Stop on the Road to Repair: Structure of E. coli DNA Ligase Bound to Nicked DNA-Adenylate.

Nandakumar, J., Nair, P.A., Shuman, S.

(2007) Mol Cell 26: 257-271

  • DOI: https://doi.org/10.1016/j.molcel.2007.02.026
  • Primary Citation Related Structures: 
    2OWO

  • PubMed Abstract: 

    NAD(+)-dependent DNA ligases (LigA) are ubiquitous in bacteria and essential for growth. Their distinctive substrate specificity and domain organization vis-a-vis human ATP-dependent ligases make them outstanding targets for anti-infective drug discovery. We report here the 2.3 A crystal structure of Escherichia coli LigA bound to an adenylylated nick, which captures LigA in a state poised for strand closure and reveals the basis for nick recognition. LigA envelopes the DNA within a protein clamp. Large protein domain movements and remodeling of the active site orchestrate progression through the three chemical steps of the ligation reaction. The structure inspires a strategy for inhibitor design.

    • Organizational Affiliation: 
    • Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10021, USA.

Macromolecule Content 

  • Total Structure Weight: 90.46 kDa 
  • Atom Count: 5,991 
  • Modeled Residue Count: 638 
  • Deposited Residue Count: 723 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 3

Macromolecules


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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA ligaseD [auth A]671Escherichia coli K-12Mutation(s): 0 
Gene Names: ligA
EC: 6.5.1.2
UniProt
Find proteins for P15042 (Escherichia coli (strain K12))
Explore P15042 
Go to UniProtKB:  P15042
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15042
Sequence Annotations
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Reference Sequence
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Entity ID: 1
MoleculeChains LengthOrganismImage
26-MERA [auth B]26N/A
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Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*AP*CP*AP*AP*TP*TP*GP*CP*GP*AP*CP*(OMC)P*C)-3'B [auth C]13N/A
Sequence Annotations
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Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
5'-D(*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*TP*G)-3'C [auth D]13N/A
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.254 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.222 (DCC) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.441α = 90
b = 99.273β = 105.33
c = 86.245γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-15
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description