3U0B

Crystal structure of an oxidoreductase from Mycobacterium smegmatis

• PDB DOI:  https://doi.org/10.2210/pdb3U0B/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-09-28 Released: 2011-10-05 
• Deposition Author(s): Arakaki, T.L., Staker, B.L., Clifton, M.C., Abendroth, J., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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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 

Literature

Increasing the structural coverage of tuberculosis drug targets.

Baugh, L., Phan, I., Begley, D.W., Clifton, M.C., Armour, B., Dranow, D.M., Taylor, B.M., Muruthi, M.M., Abendroth, J., Fairman, J.W., Fox, D., Dieterich, S.H., Staker, B.L., Gardberg, A.S., Choi, R., Hewitt, S.N., Napuli, A.J., Myers, J., Barrett, L.K., Zhang, Y., Ferrell, M., Mundt, E., Thompkins, K., Tran, N., Lyons-Abbott, S., Abramov, A., Sekar, A., Serbzhinskiy, D., Lorimer, D., Buchko, G.W., Stacy, R., Stewart, L.J., Edwards, T.E., Van Voorhis, W.C., Myler, P.J.

(2015) Tuberculosis (Edinb) 95: 142-148

• PubMed: 25613812 
• DOI: https://doi.org/10.1016/j.tube.2014.12.003
• Primary Citation of Related Structures:  
  3GVC, 3GVG, 3GWC, 3H7F, 3H81, 3HE2, 3HWI, 3HWK, 3HZG, 3ICO, 3KHP, 3LLS, 3MOY, 3MPZ, 3MYB, 3NDN, 3NDO, 3NF4, 3NG3, 3NJD, 3NWO, 3O0M, 3O38, 3OC6, 3OC7, 3OI9, 3OKS, 3OME, 3P0T, 3P2Y, 3P4I, 3P4T, 3P5M, 3P85, 3PE8, 3PK0, 3PPI, 3PZY, 3Q1T, 3Q8N, 3QBP, 3QDF, 3QHA, 3QIV, 3QK8, 3QKA, 3QLJ, 3QMJ, 3QRE, 3QUA


• PubMed Abstract: 
  

High-resolution three-dimensional structures of essential Mycobacterium tuberculosis (Mtb) proteins provide templates for TB drug design, but are available for only a small fraction of the Mtb proteome. Here we evaluate an intra-genus "homolog-rescue" strategy to increase the structural information available for TB drug discovery by using mycobacterial homologs with conserved active sites. Of 179 potential TB drug targets selected for x-ray structure determination, only 16 yielded a crystal structure. By adding 1675 homologs from nine other mycobacterial species to the pipeline, structures representing an additional 52 otherwise intractable targets were solved. To determine whether these homolog structures would be useful surrogates in TB drug design, we compared the active sites of 106 pairs of Mtb and non-TB mycobacterial (NTM) enzyme homologs with experimentally determined structures, using three metrics of active site similarity, including superposition of continuous pharmacophoric property distributions. Pair-wise structural comparisons revealed that 19/22 pairs with >55% overall sequence identity had active site Cα RMSD <1 Å, >85% side chain identity, and ≥80% PSAPF (similarity based on pharmacophoric properties) indicating highly conserved active site shape and chemistry. Applying these results to the 52 NTM structures described above, 41 shared >55% sequence identity with the Mtb target, thus increasing the effective structural coverage of the 179 Mtb targets over three-fold (from 9% to 32%). The utility of these structures in TB drug design can be tested by designing inhibitors using the homolog structure and assaying the cognate Mtb enzyme; a promising test case, Mtb cytidylate kinase, is described. The homolog-rescue strategy evaluated here for TB is also generalizable to drug targets for other diseases.

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Organizational Affiliation: 

Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States; Department of Global Health, University of Washington, Box 359931, Seattle, WA, 98195, United States; Department of Biomedical Informatics and Medical Education, University of Washington, Box 358047, Seattle, WA 98195, United States. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 46.87 kDa 
• Atom Count: 3,617 
• Modelled Residue Count: 415 
• Deposited Residue Count: 454 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidoreductase, short chain dehydrogenase/reductase family protein	A	454	Mycolicibacterium smegmatis MC2 155	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	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 = 102.73	α = 90
b = 58.22	β = 127.82
c = 76.88	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-05 
Deposition Author(s): Arakaki, T.L., Staker, B.L., Clifton, M.C., Abendroth, J., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• 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