2Q2T

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1038/nsmb1266
  • Primary Citation of Related Structures:  

  • 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 Chl ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Chlorella virus DNA ligase
A
319Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A544R
Find proteins for O41026 (Paramecium bursaria Chlorella virus 1)
Go to UniProtKB:  O41026
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*T)-3'B21N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*AP*TP*TP*GP*CP*GP*AP*CP*(OMC)P*C)-3'C10N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(P*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)-3'D11N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP

Download SDF File 
Download CCD File 
A
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OMC
Query on OMC
C
RNA LINKINGC10 H16 N3 O8 PC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 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 = 90.00
b = 81.290β = 90.00
c = 96.418γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
DENZOdata reduction
ADSCdata collection
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-07-10
    Type: Initial release
  • Version 1.1: 2007-10-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description