Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Dihedral - D4  (3D View)
Global Stoichiometry: Homo 8-mer - A8 

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

Macromolecule Content

• Total Structure Weight: 304940.78 
• Atom Count: 20549 
• Residue Count: 2720 
• Unique protein chains: 1

3SYT

Crystal structure of glutamine-dependent NAD+ synthetase from M. tuberculosis bound to AMP/PPi, NAD+, and glutamate

• DOI: 10.2210/pdb3SYT/pdb

• Classification: LIGASE
• Organism(s): Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2011-07-18 Released: 2012-04-11 
• Deposition Author(s): Chuenchor, W., Gerratana, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.6511 Å
• R-Value Free: 0.200 
• R-Value Work: 0.155 

Literature

Regulation of the intersubunit ammonia tunnel in Mycobacterium tuberculosis glutamine-dependent NAD+ synthetase.

Chuenchor, W., Doukov, T.I., Resto, M., Chang, A., Gerratana, B.

(2012) Biochem.J. 443: 417-426

• PubMed: 22280445 
• DOI: 10.1042/BJ20112210
• Primary Citation of Related Structures:  
  3SZG, 3SEZ, 3SEQ, 3SDB


• PubMed Abstract: 
  

Glutamine-dependent NAD+ synthetase is an essential enzyme and a validated drug target in Mycobacterium tuberculosis (mtuNadE). It catalyses the ATP-dependent formation of NAD+ from NaAD+ (nicotinic acid-adenine dinucleotide) at the synthetase active site and glutamine hydrolysis at the glutaminase active site. An ammonia tunnel 40 Å (1 Å=0.1 nm) long allows transfer of ammonia from one active site to the other. The enzyme displays stringent kinetic synergism; however, its regulatory mechanism is unclear. In the present paper, we report the structures of the inactive glutaminase C176A variant in an apo form and in three synthetase-ligand complexes with substrates (NaAD+/ATP), substrate analogue {NaAD+/AMP-CPP (adenosine 5'-[α,β-methylene]triphosphate)} and intermediate analogues (NaAD+/AMP/PPi), as well as the structure of wild-type mtuNadE in a product complex (NAD+/AMP/PPi/glutamate). This series of structures provides snapshots of the ammonia tunnel during the catalytic cycle supported also by kinetics and mutagenesis studies. Three major constriction sites are observed in the tunnel: (i) at the entrance near the glutaminase active site; (ii) in the middle of the tunnel; and (iii) at the end near the synthetase active site. Variation in the number and radius of the tunnel constrictions is apparent in the crystal structures and is related to ligand binding at the synthetase domain. These results provide new insight into the regulation of ammonia transport in the intermolecular tunnel of mtuNadE.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742-2021, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Glutamine-dependent NAD(+) synthetase	A, B, C, D	680	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Mutation(s): 0  Gene Names: nadE EC: 6.3.5.1
Find proteins for P9WJJ3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Go to UniProtKB:  P9WJJ3

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
POP	A, B, C, D	PYROPHOSPHATE 2- H2 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-L
GOL	A, C	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NAD	A, B, C, D	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
GLU	A, B, C, D	GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-VKHMYHEASA-N
AMP	A, B, C, D	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.6511 Å
• R-Value Free: 0.200 
• R-Value Work: 0.155 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 177.755	α = 90.00
b = 177.755	β = 90.00
c = 213.059	γ = 90.00

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
HKL-2000	data reduction
HKL-2000	data collection
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-07-18 
• Released Date: 2012-04-11 
• Deposition Author(s): Chuenchor, W., Gerratana, B.

Revision History 

• Version 1.0: 2012-04-11
  Type: Initial release
• Version 1.1: 2017-11-08
  Type: Refinement description