Biological Assembly 1  

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

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 120.95 kDa 
• Atom Count: 8648 
• Modelled Residue Count: 995 
• Deposited Residue Count: 1023 
• Unique protein chains: 1

2QJO

crystal structure of a bifunctional NMN adenylyltransferase/ADP ribose pyrophosphatase (NadM) complexed with ADPRP and NAD from Synechocystis sp.

• PDB DOI: 10.2210/pdb2QJO/pdb

• Classification: TRANSFERASE, HYDROLASE
• Organism(s): Synechocystis sp. PCC 6803
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2007-07-08 Released: 2008-03-11 
• Deposition Author(s): Huang, N., Sorci, L., Zhang, X., Brautigan, C., Raffaelli, N., Magni, G., Grishin, N.V., Osterman, A., Zhang, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.228 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 

Literature

Bifunctional NMN Adenylyltransferase/ADP-Ribose Pyrophosphatase: Structure and Function in Bacterial NAD Metabolism.

Huang, N., Sorci, L., Zhang, X., Brautigam, C.A., Li, X., Raffaelli, N., Magni, G., Grishin, N.V., Osterman, A.L., Zhang, H.

(2008) Structure 16: 196-209

• PubMed: 18275811 
• DOI: 10.1016/j.str.2007.11.017
• Primary Citation of Related Structures:  
  2QJO, 2QJT, 2R5W


• PubMed Abstract: 
  

Bacterial NadM-Nudix is a bifunctional enzyme containing a nicotinamide mononucleotide (NMN) adenylyltransferase and an ADP-ribose (ADPR) pyrophosphatase domain. While most members of this enzyme family, such as that from a model cyanobacterium Synechocystis sp., are involved primarily in nicotinamide adenine dinucleotide (NAD) salvage/recycling pathways, its close homolog in a category-A biodefense pathogen, Francisella tularensis, likely plays a central role in a recently discovered novel pathway of NAD de novo synthesis. The crystal structures of NadM-Nudix from both species, including their complexes with various ligands and catalytic metal ions, revealed detailed configurations of the substrate binding and catalytic sites in both domains. The structure of the N-terminal NadM domain may be exploited for designing new antitularemia therapeutics. The ADPR binding site in the C-terminal Nudix domain is substantially different from that of Escherichia coli ADPR pyrophosphatase, and is more similar to human NUDT9. The latter observation provided new insights into the ligand binding mode of ADPR-gated Ca2+ channel TRPM2.

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Organizational Affiliation: 

Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional NMN adenylyltransferase/Nudix hydrolase	A, B, C	341	Synechocystis sp. PCC 6803	Mutation(s): 0  Gene Names: slr0787 EC: 2.7.7.1 (PDB Primary Data), 3.6.1 (PDB Primary Data)
UniProt
Find proteins for Q55928 (Synechocystis sp. (strain PCC 6803 / Kazusa)) Explore Q55928  Go to UniProtKB:  Q55928

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	H [auth A], L [auth B], O [auth C]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
APR	G [auth A], K [auth B], N [auth C]	ADENOSINE-5-DIPHOSPHORIBOSE C15 H23 N5 O14 P2 SRNWOUGRCWSEMX-KEOHHSTQSA-N
POP	I [auth A], M [auth B], P [auth C]	PYROPHOSPHATE 2- H2 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-L
SO4	D [auth A], E [auth A], F [auth A], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.228 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 201.54	α = 90
b = 201.54	β = 90
c = 98.695	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXCD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-07-08 
• Released Date: 2008-03-11 
Deposition Author(s): Huang, N., Sorci, L., Zhang, X., Brautigan, C., Raffaelli, N., Magni, G., Grishin, N.V., Osterman, A., Zhang, H.

Revision History  

• Version 1.0: 2008-03-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-18
  Changes: Refinement description