6OFB

Crystal structure of human glutamine-dependent NAD+ synthetase complexed with NaAD+, AMP, pyrophosphate, and Mg2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Different ways to transport ammonia in human and Mycobacterium tuberculosis NAD+synthetases.

Chuenchor, W.Doukov, T.I.Chang, K.T.Resto, M.Yun, C.S.Gerratana, B.

(2020) Nat Commun 11: 16-16

  • DOI: 10.1038/s41467-019-13845-4
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • NAD <sup>+ </sup> synthetase is an essential enzyme of de novo and recycling pathways of NAD <sup>+ </sup> biosynthesis in Mycobacterium tuberculosis but not in humans. This bifunctional enzyme couples the NAD <sup>+ </sup> synthetase and glutaminase ...

    NAD + synthetase is an essential enzyme of de novo and recycling pathways of NAD + biosynthesis in Mycobacterium tuberculosis but not in humans. This bifunctional enzyme couples the NAD + synthetase and glutaminase activities through an ammonia tunnel but free ammonia is also a substrate. Here we show that the Homo sapiens NAD + synthetase (hsNadE) lacks substrate specificity for glutamine over ammonia and displays a modest activation of the glutaminase domain compared to tbNadE. We report the crystal structures of hsNadE and NAD + synthetase from M. tuberculosis (tbNadE) with synthetase intermediate analogues. Based on the observed exclusive arrangements of the domains and of the intra- or inter-subunit tunnels we propose a model for the inter-domain communication mechanism for the regulation of glutamine-dependent activity and NH 3 transport. The structural and mechanistic comparison herein reported between hsNadE and tbNadE provides also a starting point for future efforts in the development of anti-TB drugs.


    Organizational Affiliation

    Stanford Synchrotron Radiation Lightsource, Menlo Park, CA, 94025, USA.,Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon, 34114, Korea.,Departments of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA. bgerratana@hotmail.com.,Departments of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamine-dependent NAD(+) synthetase
A, B
707Homo sapiensMutation(s): 0 
Gene Names: NADSYN1
EC: 6.3.5.1
Find proteins for Q6IA69 (Homo sapiens)
Go to Gene View: NADSYN1
Go to UniProtKB:  Q6IA69
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
POP
Query on POP

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Download CCD File 
A, B
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
 Ligand Interaction
DND
Query on DND

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Download CCD File 
A, B
NICOTINIC ACID ADENINE DINUCLEOTIDE
DEAMIDO-NAD+
C21 H27 N6 O15 P2
SENPVEZBRZQVST-HISDBWNOSA-O
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
AMP
Query on AMP

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Download CCD File 
A, B
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.179 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 102.250α = 90.00
b = 198.890β = 90.00
c = 219.690γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
PHENIXphasing
SCALAdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-01-08
    Type: Initial release
  • Version 1.1: 2020-01-22
    Type: Database references