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PDBsum entry 2aqi

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Oxidoreductase PDB id
2aqi
Jmol
Contents
Protein chain
268 a.a. *
Ligands
NAI
Waters ×147
* Residue conservation analysis
PDB id:
2aqi
Name: Oxidoreductase
Title: Crystal structure of isoniazid-resistant i47t enoyl-acp(coa) mutant enzyme from mycobacterium tuberculosis in complex wi
Structure: Enoyl-[acyl-carrier-protein] reductase [nadh]. Chain: a. Synonym: nadh-dependent enoyl-acp reductase. Engineered: yes. Mutation: yes
Source: Mycobacterium tuberculosis. Organism_taxid: 1773. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Tetramer (from PDB file)
Resolution:
2.20Å     R-factor:   0.187     R-free:   0.213
Authors: J.S.Oliveira,J.H.Pereira,N.C.Rodrigues,F.Canduri,O.N.De Souz L.A.Basso,W.F.De Azevedo Jr.,D.S.Santos
Key ref:
J.S.Oliveira et al. (2006). Crystallographic and pre-steady-state kinetics studies on binding of NADH to wild-type and isoniazid-resistant enoyl-ACP(CoA) reductase enzymes from Mycobacterium tuberculosis. J Mol Biol, 359, 646-666. PubMed id: 16647717 DOI: 10.1016/j.jmb.2006.03.055
Date:
18-Aug-05     Release date:   23-May-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam  
P9WGR1  (INHA_MYCTU) -  Enoyl-[acyl-carrier-protein] reductase [NADH]
Seq:
Struc:
269 a.a.
268 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.1.3.1.9  - Enoyl-[acyl-carrier-protein] reductase (NADH).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: An acyl-[acyl-carrier protein] + NAD+ = a trans-2,3-dehydroacyl-[acyl- carrier protein] + NADH
acyl-[acyl-carrier protein]
+
NAD(+)
Bound ligand (Het Group name = NAD)
corresponds exactly
= trans-2,3-dehydroacyl-[acyl- carrier protein]
+ NADH
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   5 terms 
  Biochemical function     oxidoreductase activity     2 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2006.03.055 J Mol Biol 359:646-666 (2006)
PubMed id: 16647717  
 
 
Crystallographic and pre-steady-state kinetics studies on binding of NADH to wild-type and isoniazid-resistant enoyl-ACP(CoA) reductase enzymes from Mycobacterium tuberculosis.
J.S.Oliveira, J.H.Pereira, F.Canduri, N.C.Rodrigues, O.N.de Souza, W.F.de Azevedo, L.A.Basso, D.S.Santos.
 
  ABSTRACT  
 
An understanding of isoniazid (INH) drug resistance mechanism in Mycobacterium tuberculosis should provide significant insight for the development of newer anti-tubercular agents able to control INH-resistant tuberculosis (TB). The inhA-encoded 2-trans enoyl-acyl carrier protein reductase enzyme (InhA) has been shown through biochemical and genetic studies to be the primary target for INH. In agreement with these results, mutations in the inhA structural gene have been found in INH-resistant clinical isolates of M.tuberculosis, the causative agent of TB. In addition, the InhA mutants were shown to have higher dissociation constant values for NADH and lower values for the apparent first-order rate constant for INH inactivation as compared to wild-type InhA. Here, in trying to identify structural changes between wild-type and INH-resistant InhA enzymes, we have solved the crystal structures of wild-type and of S94A, I47T and I21V InhA proteins in complex with NADH to resolutions of, respectively, 2.3A, 2.2A, 2.0 A, and 1.9A. The more prominent structural differences are located in, and appear to indirectly affect, the dinucleotide binding loop structure. Moreover, studies on pre-steady-state kinetics of NADH binding have been carried out. The results showed that the limiting rate constant values for NADH dissociation from the InhA-NADH binary complexes (k(off)) were eleven, five, and tenfold higher for, respectively, I21V, I47T, and S94A INH-resistant mutants of InhA as compared to INH-sensitive wild-type InhA. Accordingly, these results are proposed to be able to account for the reduction in affinity for NADH for the INH-resistant InhA enzymes.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Surroundings of position 47 in the crystal structures of WT (a) and (c), I47T (b) and (d), I21V(e), and S94A(f). For clarity, only the NADH dinucleotide binding loop (Gly14-Ala22) residues, strand b2 residues Thr39 and Gly40, residues from the turn between strand b2 and helix a2 (Phe41-Arg43), Leu63, Ile47 (a) or Thr47 (b), and water molecules near the position 47 that are involved in hydrogen bond network are shown. The atoms are colored green for carbon, blue for nitrogen, red for oxygen, and magenta for phosphorus. The water molecules are numbered 1, 2, 3 and 4 and correspond to waters 272, 282, and 281 in both WT InhA and I47T InhA structures and to water 321 in I47T InhA structure, respectively. The most relevant hydrogen bonding differences between the structures of WT-NADH and I47T-NADH binary complexes are shown in (a) and (b), respectively. The (2F[obs] -F[calc]) electron density maps encompassing the residue 47 and the surrounding atoms of the structures of WT-NADH, I47T-NADH, I21V-NADH, and S94A-NADH binary complexes are shown in (c), (d), (e), and (f), respectively. The (2F[obs] -F[calc]), a[calc] maps were calculated in the REFMAC 5.2 program48 using all unique reflections and are countoured at a level of 1.2s above the mean. The Figure was prepared with CCP4 Molecular Graphics 0.12 program.62
Figure 7.
Figure 7. Scheme showing the minimum kinetic mechanism proposed for NADH binding to WT and isoniazid-resistant InhA enzymes. The fast phase corresponds to a bimolecular association between InhA (E form) and NADH. In case of NADH binding to S94A the fast phase also includes a further isomerization of E-NADH complex to E-NADH*. The rate of slow phase is limited by the slow isomerization of E* form of InhA to the E form, where only the E form binds NADH.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 359, 646-666) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21280175 K.Maity, T.Banerjee, N.Prabakaran, N.Surolia, A.Surolia, and K.Suguna (2011).
Effect of substrate binding loop mutations on the structure, kinetics, and inhibition of enoyl acyl carrier protein reductase from plasmodium falciparum.
  IUBMB Life, 63, 30-41.
PDB codes: 3am3 3am4 3am5
21094257 N.J.Singh, D.Shin, H.M.Lee, H.T.Kim, H.J.Chang, J.M.Cho, K.S.Kim, and S.Ro (2011).
Structural basis of triclosan resistance.
  J Struct Biol, 174, 173-179.
PDB codes: 3pjd 3pje 3pjf
20485741 B.A.Neto, A.A.Lapis, F.S.Mancilha, E.L.Batista, P.A.Netz, F.Rominger, L.A.Basso, D.S.Santos, and J.Dupont (2010).
On the selective detection of duplex deoxyribonucleic acids by 2,1,3-benzothiadiazole fluorophores.
  Mol Biosyst, 6, 967-975.  
17021094 F.Brossier, N.Veziris, C.Truffot-Pernot, V.Jarlier, and W.Sougakoff (2006).
Performance of the genotype MTBDR line probe assay for detection of resistance to rifampin and isoniazid in strains of Mycobacterium tuberculosis with low- and high-level resistance.
  J Clin Microbiol, 44, 3659-3664.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.