8ZB5 | pdb_00008zb5

Crystal structure of NudC from Mycobacterium abscessus in complex with AMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.269 (Depositor), 0.269 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 
    0.223 (Depositor) 

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Literature

Structural Studies on Mycobacterial NudC Reveal a Class of Zinc Independent NADH Pyrophosphatase.

Meng, L.Sun, Z.Zhang, Y.Dong, Y.Du, X.Wu, Y.Yuan, Y.Sun, Y.Xu, Y.Ding, H.Liu, J.Xu, J.

(2024) J Mol Biology 436: 168864-168864

  • DOI: https://doi.org/10.1016/j.jmb.2024.168864
  • Primary Citation of Related Structures:  
    8ZB3, 8ZB4, 8ZB5

  • PubMed Abstract: 

    Non-tuberculous mycobacteria (NTM) have emerged as an increasing threat to public health, due to the extreme antibiotic resistance. NADH pyrophosphatase (NudC) was proposed involving in mycobacterial resistance to the first line anti-tubercular drug isoniazid (INH) or its analog ethionamide (ETH), by hydrolyzing their NAD modified active forms (NAD-INH and NAD-ETH). In this study, we performed enzymatic and structural studies on NudC from M. abscessus (NudC Mab ), which is highly resistant to isoniazid and emerging as the most worrisome NTM. We determined the crystal structures of NudC Mab in apo form, substrate NAD-bound form and product AMP-bound form. We observed the mode for the Nudix motif of NudC Mab capturing the pyrophosphate group of NAD mediated by three divalent cation ions, which provides details for understanding the mechanism on NudC hydrolyzing NAD(H) or NAD-capped substrate. Interestingly, our structures revealed a novel subclass NudC from mycobacteria characterized by a unique arginine residue on the conserved QPWPFPxS motif, as well as a unique tower domain that replaces a well-defined zinc-binding motif in E.coli NudC and catalytic domain of mammalian Nudt12. Thus, our structural studies on NudC Mab not only present a class of zinc independent NADH pyrophosphatase in mycobacteria, but also may facilitate the design of NudC inhibitors for the treatment of mycobacteria infections in combination with INH or ETH.


  • Organizational Affiliation
    • Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China; State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(+) diphosphataseA [auth B],
B [auth A]
318Mycobacteroides abscessusMutation(s): 0 
Gene Names: nudCD2E76_25755ERS075579_02720ERS075604_04155
EC: 3.6.1.22
UniProt
Find proteins for A0A0U1C370 (Mycobacteroides abscessus)
Explore A0A0U1C370 
Go to UniProtKB:  A0A0U1C370
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0U1C370
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AMP (Subject of Investigation/LOI)
Query on AMP

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

Download Ideal Coordinates CCD File 
K [auth B],
S [auth A]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
C [auth B]
D [auth B]
E [auth B]
F [auth B]
G [auth B]
C [auth B],
D [auth B],
E [auth B],
F [auth B],
G [auth B],
H [auth B],
I [auth B],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.269 (Depositor), 0.269 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 0.223 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.999α = 90
b = 131.999β = 90
c = 174.314γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
MOLREPphasing
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentChinaSKLRD-Z-20241

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-11
    Type: Initial release