2Q2T

Structure of Chlorella virus DNA ligase-adenylate bound to a 5' phosphorylated nick


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.214 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history


Literature

Structural basis for nick recognition by a minimal pluripotent DNA ligase.

Nair, P.A.Nandakumar, J.Smith, P.Odell, M.Lima, C.D.Shuman, S.

(2007) Nat Struct Mol Biol 14: 770-778

  • DOI: https://doi.org/10.1038/nsmb1266
  • Primary Citation of Related Structures:  
    2Q2T, 2Q2U

  • PubMed Abstract: 

    Chlorella virus DNA ligase, the smallest eukaryotic ligase known, has pluripotent biological activity and an intrinsic nick-sensing function, despite having none of the accessory domains found in cellular ligases. A 2.3-A crystal structure of the Chlorella virus ligase-AMP intermediate bound to duplex DNA containing a 3'-OH-5'-PO4 nick reveals a new mode of DNA envelopment, in which a short surface loop emanating from the OB domain forms a beta-hairpin 'latch' that inserts into the DNA major groove flanking the nick. A network of interactions with the 3'-OH and 5'-PO4 termini in the active site illuminates the DNA adenylylation mechanism and the crucial roles of AMP in nick sensing and catalysis. Addition of a divalent cation triggered nick sealing in crystallo, establishing that the nick complex is a bona fide intermediate in the DNA repair pathway.


  • Organizational Affiliation

    Molecular Biology and Structural Biology Programs, Sloan-Kettering Institute, New York, New York 10021, USA.


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorella virus DNA ligaseD [auth A]319Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A544R
UniProt
Find proteins for O41026 (Paramecium bursaria Chlorella virus 1)
Explore O41026 
Go to UniProtKB:  O41026
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO41026
Sequence Annotations
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Entity ID: 1
MoleculeChains LengthOrganismImage
5'-D(*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*T)-3'A [auth B]21N/A
Sequence Annotations
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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*AP*TP*TP*GP*CP*GP*AP*CP*(OMC)P*C)-3'B [auth C]10N/A
Sequence Annotations
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Entity ID: 3
MoleculeChains LengthOrganismImage
5'-D(P*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)-3'C [auth D]11N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP

Download Ideal Coordinates CCD File 
E [auth A]ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.301α = 90
b = 81.29β = 90
c = 96.418γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-07-10
    Type: Initial release
  • Version 1.1: 2007-10-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: 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
  • Version 1.5: 2024-10-30
    Changes: Structure summary