Crystal Structure of NAD+ Synthetase from Staphylococcus aureus

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

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Crystallographic and molecular dynamics simulation analysis of NAD synthetase from methicillin resistant Staphylococcus aureus (MRSA).

Sultana, K.N.Kuldeep, J.Siddiqi, M.I.Srivastava, S.K.

(2020) Int J Biol Macromol 165: 2349-2362

  • DOI: https://doi.org/10.1016/j.ijbiomac.2020.10.096
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    NAD synthetase (NadE) catalyzes the last step in NAD biosynthesis, transforming deamido-NAD + into NAD + by a two-step reaction with co-substrates ATP and amide donor ammonia. In this study, we report the crystal structure of Staphylococcus aureus NAD synthetase enzyme (saNadE) at 2.3 Å resolution. We used this structure to perform molecular dynamics simulations of apo-enzyme, enzyme-substrate (NadE with ATP and NaAD) and enzyme-intermediate complexes (NadE with NaAD-AMP) to investigate key binding interactions and explore the conformational transitions and flexibility of the binding pocket. Our results show large shift of N-terminal region in substrate bound form which is important for ATP binding. Substrates drive the correlated movement of loop regions surrounding it as well as some regions distal to the active site and stabilize them at complex state. Principal component analysis of atomic projections distinguish feasible trajectories to delineate distinct motions in enzyme-substrate to enzyme-intermediate states. Our results suggest mixed binding involving dominant induced fit and conformational selection. MD simulation extracted ensembles of NadE could potentially be utilized for in silico screening and structure based design of more effective Methicillin Resistant Staphylococcus aureus (MRSA) inhibitors.

  • Organizational Affiliation

    Department of Biosciences, Manipal University Jaipur, Dehmi Kalan, Off Jaipur-Ajmer Expressway, Jaipur, Rajasthan 303007, India.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NH(3)-dependent NAD(+) synthetaseA,
B [auth C],
C [auth B],
281Staphylococcus aureus subsp. aureus COLMutation(s): 0 
Gene Names: nadESACOL1974
Find proteins for Q5HEK9 (Staphylococcus aureus (strain COL))
Explore Q5HEK9 
Go to UniProtKB:  Q5HEK9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5HEK9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.979α = 90
b = 107.714β = 96.72
c = 93.986γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
DIALSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Department of Biotechnology (India)IndiaBT/BI/12/045/2008

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-09
    Type: Initial release
  • Version 1.1: 2020-11-11
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description