1TA8

Structural rearrangement accompanying NAD+ synthesis within a bacterial DNA ligase crystal


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural rearrangement accompanying NAD+ synthesis within a bacterial DNA ligase crystal.

Gajiwala, K.S.Pinko, C.

(2004) STRUCTURE 12: 1449-1459

  • DOI: 10.1016/j.str.2004.05.017
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • DNA ligase is an enzyme important for DNA repair and replication. Eukaryotic genomes encode ligases requiring ATP as the cofactor; bacterial genomes encode NAD(+)-dependent ligase. This difference in substrate specificities and the essentiality of NA ...

    DNA ligase is an enzyme important for DNA repair and replication. Eukaryotic genomes encode ligases requiring ATP as the cofactor; bacterial genomes encode NAD(+)-dependent ligase. This difference in substrate specificities and the essentiality of NAD(+)-dependent ligase for bacterial survival make NAD(+)-dependent ligase a good target for designing highly specific anti-infectives. Any such structure-guided effort would require the knowledge of the precise mechanism of NAD+ recognition by the enzyme. We report the principles of NAD+ recognition by presenting the synthesis of NAD+ from nicotinamide mononucleotide (NMN) and AMP, catalyzed by Enterococcus faecalis ligase within the crystal lattice. Unprecedented conformational change, required to reorient the two subdomains of the protein for the condensation to occur and to recognize NAD+, is captured in two structures obtained using the same protein crystal. Structural data and sequence analysis presented here confirms and extends prior functional studies of the ligase adenylation reaction.


    Related Citations: 
    • Crystal structure of NAD+-dependent DNA ligase: modular architecture and functional implications.
      Lee, J.Y.,Chang, C.,Song, H.K.,Moon, J.,Yang, J.K.,Kim, H.K.,Kwon, S.T.,Suh, S.W.
      (2000) Embo J. 19: 1119
    • Structure of the adenylation domain of an NAD dependent DNA ligase
      Singleton, M.R.,Hakansson, K.,Timson, D.J.,Wigley, D.B.
      (1999) Structure 7: 35


    Organizational Affiliation

    Quorex Pharmaceuticals, 1890 Rutherford Road, Suite 200, Carlsbad, California 92008, USA. ketang@quorex.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA ligase, NAD-dependent
A
332Enterococcus faecalis (strain ATCC 700802 / V583)Mutation(s): 0 
Gene Names: ligA
EC: 6.5.1.2
Find proteins for Q837V6 (Enterococcus faecalis (strain ATCC 700802 / V583))
Go to UniProtKB:  Q837V6
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NMN
Query on NMN

Download SDF File 
Download CCD File 
A
BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE
NICOTINAMIDE MONONUCLEOTIDE
C11 H16 N2 O8 P
DAYLJWODMCOQEW-TURQNECASA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 90.167α = 90.00
b = 86.105β = 100.99
c = 57.108γ = 90.00
Software Package:
Software NamePurpose
CNXrefinement
CNXphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-11-23
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance
  • Version 1.3: 2018-01-31
    Type: Experimental preparation