1K4M

Crystal structure of E.coli nicotinic acid mononucleotide adenylyltransferase complexed to deamido-NAD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of E. coli nicotinate mononucleotide adenylyltransferase and its complex with deamido-NAD.

Zhang, H.Zhou, T.Kurnasov, O.Cheek, S.Grishin, N.V.Osterman, A.

(2002) Structure 10: 69-79

  • Primary Citation of Related Structures:  1K4K

  • PubMed Abstract: 
  • Nicotinamide/Nicotinate mononucleotide (NMN/NaMN) adenylyltransferase is an indispensable enzyme in both de novo biosynthesis and salvage of NAD+ and NADP+. In prokaryotes, it is absolutely required for cell survival, thus representing an attractive ...

    Nicotinamide/Nicotinate mononucleotide (NMN/NaMN) adenylyltransferase is an indispensable enzyme in both de novo biosynthesis and salvage of NAD+ and NADP+. In prokaryotes, it is absolutely required for cell survival, thus representing an attractive target for the development of new broad-spectrum antibacteria inhibitors. The crystal structures of E. coli NaMN adenylyltransferase (NMNAT) and its complex with deamido-NAD (NaAD) revealed that ligand binding causes large conformational changes in several loop regions around the active site. The enzyme specifically recognizes the deamidated pyridine nucleotide through interactions between nicotinate carboxylate with several protein main chain amides and a positive helix dipole. Comparison of E. coli NMNAT with those from archaeal organisms revealed extensive differences in the active site architecture, enzyme-ligand interaction mode, and bound dinucleotide conformations. The bacterial NaMN adenylyltransferase structures described here provide a foundation for structure-based design of specific inhibitors that may have therapeutic potential.


    Organizational Affiliation

    Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA. zhang@chop.swmed.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NaMN adenylyltransferase
A, B, C
213Escherichia coli (strain K12)Gene Names: nadD (ybeN)
EC: 2.7.7.18
Find proteins for P0A752 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A752
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
A, B, C
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, B, C
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.206 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 114.830α = 90.00
b = 113.930β = 90.00
c = 115.670γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
AMoREphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-10-08
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance