3U0B

Crystal structure of an oxidoreductase from Mycobacterium smegmatis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.138 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

Structural and functional characterization of FabG4 from Mycolicibacterium smegmatis.

Ran, X.Parikh, P.Abendroth, J.Arakaki, T.L.Clifton, M.C.Edwards, T.E.Lorimer, D.D.Mayclin, S.Staker, B.L.Myler, P.McLaughlin, K.J.

(2024) Acta Crystallogr F Struct Biol Commun 80: 82-91

  • DOI: https://doi.org/10.1107/S2053230X2400356X
  • Primary Citation of Related Structures:  
    3U0B, 5VP5

  • PubMed Abstract: 

    The rise in antimicrobial resistance is a global health crisis and necessitates the development of novel strategies to treat infections. For example, in 2022 tuberculosis (TB) was the second leading infectious killer after COVID-19, with multi-drug-resistant strains of TB having an ∼40% fatality rate. Targeting essential biosynthetic pathways in pathogens has proven to be successful for the development of novel antimicrobial treatments. Fatty-acid synthesis (FAS) in bacteria proceeds via the type II pathway, which is substantially different from the type I pathway utilized in animals. This makes bacterial fatty-acid biosynthesis (Fab) enzymes appealing as drug targets. FabG is an essential FASII enzyme, and some bacteria, such as Mycobacterium tuberculosis, the causative agent of TB, harbor multiple homologs. FabG4 is a conserved, high-molecular-weight FabG (HMwFabG) that was first identified in M. tuberculosis and is distinct from the canonical low-molecular-weight FabG. Here, structural and functional analyses of Mycolicibacterium smegmatis FabG4, the third HMwFabG studied to date, are reported. Crystal structures of NAD + and apo MsFabG4, along with kinetic analyses, show that MsFabG4 preferentially binds and uses NADH when reducing CoA substrates. As M. smegmatis is often used as a model organism for M. tuberculosis, these studies may aid the development of drugs to treat TB and add to the growing body of research that distinguish HMwFabGs from the archetypal low-molecular-weight FabG.


  • Organizational Affiliation

    Department of Chemistry, Vassar College, 124 Raymond Avenue, Poughkeepsie, NY 12604, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Oxidoreductase, short chain dehydrogenase/reductase family protein454Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: MSMEG_0372
UniProt
Find proteins for A0QPE7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QPE7 
Go to UniProtKB:  A0QPE7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0QPE7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download Ideal Coordinates CCD File 
B [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.138 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.73α = 90
b = 58.22β = 127.82
c = 76.88γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-05
    Type: Initial release
  • Version 1.1: 2015-03-11
    Changes: Database references
  • Version 1.2: 2015-04-15
    Changes: Database references
  • Version 1.3: 2016-05-25
    Changes: Structure summary
  • Version 1.4: 2018-03-07
    Changes: Data collection
  • Version 1.5: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.6: 2024-07-17
    Changes: Database references