3R4T

Crystal structure of 4-aminobutyrate aminotransferase GabT from Mycobacterium marinum covalently bound to pyridoxal phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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

  • DOI: 10.1016/j.tube.2014.12.003
  • Primary Citation of Related Structures:  
  • Also Cited By: 3NJB, 5EJ2, 3TSC, 3TK1, 3T7C, 3SX2, 3S55, 3QI6, 3QHX, 3QH4, 3PXX, 3PGX, 3PFD, 3P96, 3P3A, 3OIB, 3OEC, 3NXS, 3NFW, 3MD0, 3HZU, 3HGB

  • 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 ...

    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.


    Organizational Affiliation

    Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States.,Seattle Structural Genomics Center for Infectious Disease, United States; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, United States.,Seattle Structural Genomics Center for Infectious Disease, United States; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, 750 Republican Street, E-701, Box 358061, Seattle, WA 98109, United States.,Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States.,Seattle Structural Genomics Center for Infectious Disease, United States; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, 750 Republican Street, E-701, Box 358061, Seattle, WA 98109, United States; Department of Global Health, University of Washington, Box 359931, Seattle, WA, 98195, United States; Department of Microbiology, University of Washington, Box 357735, Seattle, WA 98195, United States.,Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States.,Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States; EMD Serono Research & Development Institute, Inc., 45A Middlesex Turnpike, Billerica, MA 01821, United States.,Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States; Institute for Protein Design, University of Washington, Box 357350, Seattle, WA 98195, United States.,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: peter.myler@seattlebiomed.org.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
4-aminobutyrate aminotransferase GabT
A
467Mycobacterium marinum (strain ATCC BAA-535 / M)Mutation(s): 0 
Gene Names: gabT
Find proteins for B2HN70 (Mycobacterium marinum (strain ATCC BAA-535 / M))
Go to UniProtKB:  B2HN70
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
A
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 123.620α = 90.00
b = 123.620β = 90.00
c = 157.590γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
BOSdata collection
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-03-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2015-04-22
    Type: Database references
  • Version 1.3: 2017-10-11
    Type: Data collection