Biological Assembly 1  

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Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 188453.30 
• Atom Count: 13125 
• Residue Count: 1812 
• Unique protein chains: 1

4FFC

Crystal structure of a 4-aminobutyrate aminotransferase (GabT) from Mycobacterium abscessus

• DOI: 10.2210/pdb4FFC/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacteroides abscessus (strain ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543)
• Expression System: Escherichia coli


• Deposited: 2012-05-31 Released: 2012-06-13 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.167 
• R-Value Work: 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: 10.1016/j.tube.2014.12.003
• Primary Citation of Related Structures:  
  3U0B, 3P0T, 3NG3, 3NDO, 3KHP, 3TJR, 4O2D, 4LGV, 4KAM, 4J5I, 4IZ9, 4IV6, 4IJN, 4I1Y, 4HR3, 4HDT, 4GK6, 4F47, 4F3W, 4EYE, 4EO9, 4EMD, 4EGF, 4EGE, 4ED4, 4DXL, 4DQ8, 4DIE, 4DI1, 3UWR, 3UVE, 3UCX, 3U0A, 3TZU, 3TZQ, 3TX2, 3TRR, 3TLF, 3TL3, 3TDE,
  3U0B, 3P0T, 3NG3, 3NDO, 3KHP, 3TJR, 4O2D, 4LGV, 4KAM, 4J5I, 4IZ9, 4IV6, 4IJN, 4I1Y, 4HR3, 4HDT, 4GK6, 4F47, 4F3W, 4EYE, 4EO9, 4EMD, 4EGF, 4EGE, 4ED4, 4DXL, 4DQ8, 4DIE, 4DI1, 3UWR, 3UVE, 3UCX, 3U0A, 3TZU, 3TZQ, 3TX2, 3TRR, 3TLF, 3TL3, 3TDE, 3TCR, 3TAV, 3T3W, 3SWX, 3SWT, 3SWO, 3SVT, 3SVK, 3SLL, 3SF6, 3SBX, 3S82, 3RV2, 3RSI, 3RRV, 3RRP, 3RR6, 3RR2, 3RIH, 3RFQ, 3RD8, 3RD7, 3RD5, 3R9T, 3R9S, 3R9R, 3R9Q, 3R9P, 3R8C, 3R7K, 3R6O, 3R6H, 3R4T, 3R2N, 3R20, 3R1J, 3R1I, 3R0O, 3QYR, 3QXZ, 3QXI, 3QUV, 3QUA, 3QRE, 3QMJ, 3QLJ, 3QKA, 3QK8, 3QIV, 3QHA, 3QDF, 3QBP, 3Q8N, 3Q1T, 3PZY, 3PPI, 3PK0, 3PE8, 3P85, 3P5M, 3P4T, 3P4I, 3P2Y, 3OME, 3OL4, 3OL3, 3OKS, 3OI9, 3OC7, 3OC6, 3O38, 3O0M, 3NWO, 3NJD, 3NF4, 3NDN, 3MYB, 3MPZ, 3MOY, 3LLS, 3ICO, 3HZG, 3HWK, 3HWI, 3HE2, 3H81, 3H7F, 3GWC, 3GVG, 3GVC
• 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" 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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
4-aminobutyrate aminotransferase (GabT)	A, B, C, D	453	Mycobacteroides abscessus (strain ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543)	Mutation(s): 0
Find proteins for B1MIQ9 (Mycobacteroides abscessus (strain ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543)) Go to UniProtKB:  B1MIQ9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
EDO	A, C	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B, C, D	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.167 
• R-Value Work: 0.138 
• Space Group: P 1
• Diffraction Data DOI: 
  10.18430/M34FFC Protein Diffraction

Unit Cell:

Length (Å)	Angle (°)
a = 67.400	α = 78.06
b = 67.530	β = 81.26
c = 102.460	γ = 77.44

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-05-31 
• Released Date: 2012-06-13 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History 

• Version 1.0: 2012-06-13
  Type: Initial release
• Version 1.1: 2015-03-11
  Type: Database references
• Version 1.2: 2015-04-15
  Type: Database references