6JBZ

Structural analysis of molybdopterin synthases from two mycobacteria pathogens


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural analysis of molybdopterin synthases from two mycobacterial pathogens.

Wang, H.Chen, X.Zhang, W.Zhou, W.Liu, X.Rao, Z.

(2019) Biochem Biophys Res Commun 511: 21-27

  • DOI: 10.1016/j.bbrc.2019.02.024
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The molybdenum cofactor, composed of molybdopterin and molybdenum, is a necessary compound for the catalytic activity of molybdenum enzymes. Molybdenum cofactor biosynthesis is a conserved multi-step process involving several enzymes. Molybdopterin s ...

    The molybdenum cofactor, composed of molybdopterin and molybdenum, is a necessary compound for the catalytic activity of molybdenum enzymes. Molybdenum cofactor biosynthesis is a conserved multi-step process involving several enzymes. Molybdopterin synthase, a hetero-tetrameric enzyme composed of a pair of MoaE-MoaD subunits, catalyzes the generation of the cis-dithiolene group of molybdopterin in the second step of the process. The cis-dithiolene group can covalently bind molybdenum. Most mycobacterial species possess several genes encoding the full pathway of molybdenum cofactor biosynthesis. In M. smegmatis, the moaD2 and moaE2 genes encode the functional molybdopterin synthase. However, M. tuberculosis has genes encoding several molybdopterin synthase subunit homologs, including moaD1, moaD2, moaE1, moaE2, and moaX, which encodes a MoaD-MoaE fusion protein. Previous studies have shown that moaD2 and moaE2 encode functional molybdopterin synthase. Here, we report the crystal structures of two substrate-free molybdopterin synthases from two different mycobacterial pathogens, M. tuberculosis and M. smegmatis, at 2.1 Å and 2.6 Å resolutions, respectively. The overall structure of both molybdopterin synthases was hetero-tetrameric, consisting of a MoaE2 dimer flanked on either side by single MoaD2 subunits. The carboxyl-terminal domain of MoaD2 inserted into MoaE2, forming the active pocket. A comparison with previously reported molybdopterin synthase structures showed that substrate-binding and catalytic residues were conserved, despite low sequence similarity among these enzymes. The low sequence identity at the MoaE-MoaD heterodimer interface may provide the structural basis to explore mycobacterial inhibitors.


    Organizational Affiliation

    State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China; College of Life Science, Nankai University, Tianjin, China; Laboratory of Structural Biology, Tsinghua University, Beijing, China.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MoaD/ThiS family proteinB, D92Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
Find proteins for A0A045H6C3 (Mycobacterium tuberculosis)
Explore A0A045H6C3 
Go to UniProtKB:  A0A045H6C3
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Molybdenum cofactor biosynthesis protein EA, C141Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
EC: 2.8.1.12
Find proteins for A0A045HUW8 (Mycobacterium tuberculosis)
Explore A0A045HUW8 
Go to UniProtKB:  A0A045HUW8
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.076α = 90
b = 114.076β = 90
c = 121.369γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-01-27 
  • Released Date: 2019-02-13 
  • Deposition Author(s): Wang, H.Y., Liu, X.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChinaNos. 813300237 and 81520108019

Revision History 

  • Version 1.0: 2019-02-13
    Type: Initial release
  • Version 1.1: 2019-03-06
    Changes: Data collection, Database references
  • Version 1.2: 2019-03-13
    Changes: Data collection, Database references