3ZTV

Structure of Haemophilus influenzae NAD nucleotidase (NadN)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

The High-Resolution Crystal Structure of Periplasmic Haemophilus Influenzae Nad Nucleotidase Reveals a Novel Enzymatic Function of Human Cd73 Related to Nad Metabolism.

Garavaglia, S., Bruzzone, S., Cassani, C., Canella, L., Allegrone, G., Sturla, L., Mannino, E., Millo, E., De Flora, A., Rizzi, M.

(2012) Biochem.J. 441: 131

  • DOI: 10.1042/BJ20111263
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Haemophilus influenzae is a major pathogen of the respiratory tract in humans that has developed the capability to exploit host NAD(P) for its nicotinamide dinucleotide requirement. This strategy is organized around a periplasmic enzyme termed NadN ( ...

    Haemophilus influenzae is a major pathogen of the respiratory tract in humans that has developed the capability to exploit host NAD(P) for its nicotinamide dinucleotide requirement. This strategy is organized around a periplasmic enzyme termed NadN (NAD nucleotidase), which plays a central role by degrading NAD into adenosine and NR (nicotinamide riboside), the latter being subsequently internalized by a specific permease. We performed a biochemical and structural investigation on H. influenzae NadN which determined that the enzyme is a Zn2+-dependent 5'-nucleotidase also endowed with NAD(P) pyrophosphatase activity. A 1.3 Å resolution structural analysis revealed a remarkable conformational change that occurs during catalysis between the open and closed forms of the enzyme. NadN showed a broad substrate specificity, recognizing either mono- or di-nucleotide nicotinamides and different adenosine phosphates with a maximal activity on 5'-adenosine monophosphate. Sequence and structural analysis of H. influenzae NadN led us to discover that human CD73 is capable of processing both NAD and NMN, therefore disclosing a possible novel function of human CD73 in systemic NAD metabolism. Our data may prove to be useful for inhibitor design and disclosed unanticipated fascinating evolutionary relationships.

    Organizational Affiliation: 

    Dipartimento di Scienze Chimiche, Alimentari, Farmaceutiche e Farmacologiche, University of Piemonte Orientale Amedeo Avogadro, Via Bovio 6, 28100 Novara, Italy. silvia.garavaglia@pharm.unipmn.it




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NAD NUCLEOTIDASE
A
579Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)Mutation(s): 0 
EC: 3.1.3.5
Find proteins for P44569 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd))
Go to UniProtKB:  P44569
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 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
ADN
Query on ADN
Download SDF File 
Download CCD File 
A
ADENOSINE
C10 H13 N5 O4
OIRDTQYFTABQOQ-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.200 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 54.640α = 90.00
b = 126.607β = 90.00
c = 200.486γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
SCALAdata scaling
PHENIXrefinement
MOSFLMdata reduction

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-14
    Type: Initial release
  • Version 1.1: 2011-12-28
    Type: Other