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 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1038/s41467-019-13845-4
  • Primary Citation of Related Structures:  
    6OFB, 6OFC

  • PubMed Abstract: 

    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

    Departments of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamine-dependent NAD(+) synthetase
A, B
707Homo sapiensMutation(s): 2 
Gene Names: NADSYN1
EC: 6.3.5.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q6IA69 (Homo sapiens)
Explore Q6IA69 
Go to UniProtKB:  Q6IA69
PHAROS:  Q6IA69
GTEx:  ENSG00000172890 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6IA69
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DND (Subject of Investigation/LOI)
Query on DND

Download Ideal Coordinates CCD File 
C [auth A],
L [auth B]
NICOTINIC ACID ADENINE DINUCLEOTIDE
C21 H27 N6 O15 P2
SENPVEZBRZQVST-HISDBWNOSA-O
AMP (Subject of Investigation/LOI)
Query on AMP

Download Ideal Coordinates CCD File 
D [auth A],
M [auth B]
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
POP (Subject of Investigation/LOI)
Query on POP

Download Ideal Coordinates CCD File 
E [auth A],
N [auth B]
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
P [auth B],
Q [auth B],
R [auth B],
S [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
F [auth A],
O [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.25α = 90
b = 198.89β = 90
c = 219.69γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-08
    Type: Initial release
  • Version 1.1: 2020-01-22
    Changes: Database references
  • Version 1.2: 2023-02-01
    Changes: Advisory, Database references, Derived calculations
  • Version 1.3: 2023-10-25
    Changes: Data collection, Refinement description