4FB8 | pdb_00004fb8

Crystal Structure of apo Acyl-CoA Carboxylase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.304 (Depositor), 0.293 (DCC) 
  • R-Value Work: 
    0.233 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 
    0.236 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Structure, Activity, and Inhibition of the Carboxyltransferase beta-Subunit of Acetyl Coenzyme A Carboxylase (AccD6) from Mycobacterium tuberculosis.

Reddy, M.C.Breda, A.Bruning, J.B.Sherekar, M.Valluru, S.Thurman, C.Ehrenfeld, H.Sacchettini, J.C.

(2014) Antimicrob Agents Chemother 58: 6122-6132

  • DOI: https://doi.org/10.1128/AAC.02574-13
  • Primary Citation Related Structures: 
    4FB8, 4G2R

  • PubMed Abstract: 

    In Mycobacterium tuberculosis, the carboxylation of acetyl coenzyme A (acetyl-CoA) to produce malonyl-CoA, a building block in long-chain fatty acid biosynthesis, is catalyzed by two enzymes working sequentially: a biotin carboxylase (AccA) and a carboxyltransferase (AccD). While the exact roles of the three different biotin carboxylases (AccA1 to -3) and the six carboxyltransferases (AccD1 to -6) in M. tuberculosis are still not clear, AccD6 in complex with AccA3 can synthesize malonyl-CoA from acetyl-CoA. A series of 10 herbicides that target plant acetyl-CoA carboxylases (ACC) were tested for inhibition of AccD6 and for whole-cell activity against M. tuberculosis. From the tested herbicides, haloxyfop, an arylophenoxypropionate, showed in vitro inhibition of M. tuberculosis AccD6, with a 50% inhibitory concentration (IC50) of 21.4 ± 1 μM. Here, we report the crystal structures of M. tuberculosis AccD6 in the apo form (3.0 Å) and in complex with haloxyfop-R (2.3 Å). The structure of M. tuberculosis AccD6 in complex with haloxyfop-R shows two molecules of the inhibitor bound on each AccD6 subunit. These results indicate the potential for developing novel therapeutics for tuberculosis based on herbicides with low human toxicity.


  • Organizational Affiliation
    • Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA.

Macromolecule Content 

  • Total Structure Weight: 100.4 kDa 
  • Atom Count: 6,220 
  • Modeled Residue Count: 862 
  • Deposited Residue Count: 946 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Probable propionyl-CoA carboxylase beta chain 6
A, B
473Mycobacterium tuberculosisMutation(s): 0 
Gene Names: accD6MT2307MTCY427.28Rv2247
EC: 6.4.1.3 (PDB Primary Data), 2.1.3.15 (UniProt), 2.1.3 (UniProt)
UniProt
Find proteins for P9WQH5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WQH5 
Go to UniProtKB:  P9WQH5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WQH5
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.304 (Depositor), 0.293 (DCC) 
  • R-Value Work:  0.233 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 0.236 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.284α = 90
b = 82.361β = 90
c = 157.87γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-19
    Type: Initial release
  • Version 1.1: 2014-08-13
    Changes: Database references
  • Version 1.2: 2014-10-01
    Changes: Database references
  • Version 1.3: 2017-11-15
    Changes: Refinement description
  • Version 1.4: 2023-09-13
    Changes: Data collection, Database references, Refinement description