Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 64.25 kDa 
• Atom Count: 5047 
• Modelled Residue Count: 565 
• Deposited Residue Count: 579 
• Unique protein chains: 1

3ZTV

Structure of Haemophilus influenzae NAD nucleotidase (NadN)

• PDB DOI: 10.2210/pdb3ZTV/pdb

• Classification: HYDROLASE
• Organism(s): Haemophilus influenzae Rd KW20
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-07-12 Released: 2011-12-14 
• Deposition Author(s): Garavaglia, S., Bruzzone, S., Cassani, C., Canella, L., Allegrone, G., Sturla, L., Mannino, E., Millo, E., De Flora, A., Rizzi, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.234 
• R-Value Work: 0.200 
• R-Value Observed: 0.201 

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

• PubMed: 21933152 
• DOI: 10.1042/BJ20111263
• Primary Citation of Related Structures:  
  3ZTV, 3ZU0


• 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 (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.

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Organizational Affiliation: 

Dipartimento di Scienze Chimiche, Alimentari, Farmaceutiche e Farmacologiche, University of Piemonte Orientale Amedeo Avogadro, Via Bovio 6, 28100 Novara, Italy. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD NUCLEOTIDASE	A	579	Haemophilus influenzae Rd KW20	Mutation(s): 0  Gene Names: HI_0206 EC: 3.1.3.5
UniProt
Find proteins for P44569 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)) Explore P44569  Go to UniProtKB:  P44569

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADN	D [auth A]	ADENOSINE C10 H13 N5 O4 OIRDTQYFTABQOQ-KQYNXXCUSA-N
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.234 
• R-Value Work: 0.200 
• R-Value Observed: 0.201 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.64	α = 90
b = 126.607	β = 90
c = 200.486	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-07-12 
• Released Date: 2011-12-14 
Deposition Author(s): Garavaglia, S., Bruzzone, S., Cassani, C., Canella, L., Allegrone, G., Sturla, L., Mannino, E., Millo, E., De Flora, A., Rizzi, M.

Revision History  

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