PDBsum entry 4rlt

Lyase/lyase inhibitor

PDB id: 4rlt

Contents

Protein chains

155 a.a.

147 a.a.

Ligands

FSE

GOL ×2

Waters ×245

PDB id:

4rlt

Name:

Lyase/lyase inhibitor

Title:

Crystal structure of (3r)-hydroxyacyl-acp dehydratase hadab hetero- dimer from mycobacterium tuberculosis complexed with fisetin

Structure:

(3r)-hydroxyacyl-acp dehydratase subunit hada. Chain: a. Synonym: rv0635. Engineered: yes. (3r)-hydroxyacyl-acp dehydratase subunit hadb. Chain: b. Synonym: rv0636. Engineered: yes

Source:

Mycobacterium tuberculosis h37rv. Organism_taxid: 83332. Gene: hada, p425_00663, rvbd_0635. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: hadb, p425_00664, rv0636, rvbd_0636.

Resolution:

2.05Å R-factor: 0.159 R-free: 0.190

Authors:

J.Li,Y.Dong,Z.H.Rao

Key ref:

Y.Dong et al. (2015). Molecular basis for the inhibition of β-hydroxyacyl-ACP dehydratase HadAB complex from Mycobacterium tuberculosis by flavonoid inhibitors. Protein Cell, 6, 504-517. PubMed id: 26081470 DOI: 10.1007/s13238-015-0181-1

Date:

18-Oct-14 Release date: 21-Oct-15

Protein chain

P9WFK1  (Y635_MYCTU) -  UPF0336 protein Rv0635 from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

Seq: 158 a.a.

Struc: 155 a.a.*

Protein chain

I6WYY7  (I6WYY7_MYCTU) -  (3R)-hydroxyacyl-ACP dehydratase subunit HadB from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

Seq: 142 a.a.

Struc: 147 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: Chains A, B: E.C.4.2.1.59 - 3-hydroxyacyl-[acyl-carrier-protein] dehydratase.
• Reaction: a (3R)-hydroxyacyl-[ACP] = a (2E)-enoyl-[ACP] + H2O

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Key reference

DOI no: 10.1007/s13238-015-0181-1

Protein Cell 6:504-517 (2015)

PubMed id: 26081470

Molecular basis for the inhibition of β-hydroxyacyl-ACP dehydratase HadAB complex from Mycobacterium tuberculosis by flavonoid inhibitors.

Y.Dong, X.Qiu, N.Shaw, Y.Xu, Y.Sun, X.Li, J.Li, Z.Rao.

ABSTRACT

Dehydration is one of the key steps in the biosynthesis of mycolic acids and is vital to the growth of Mycobacterium tuberculosis (Mtb). Consequently, stalling dehydration cures tuberculosis (TB). Clinically used anti-TB drugs like thiacetazone (TAC) and isoxyl (ISO) as well as flavonoids inhibit the enzyme activity of the β-hydroxyacyl-ACP dehydratase HadAB complex. How this inhibition is exerted, has remained an enigma for years. Here, we describe the first crystal structures of the MtbHadAB complex bound with flavonoid inhibitor butein, 2',4,4'-trihydroxychalcone or fisetin. Despite sharing no sequence identity from Blast, HadA and HadB adopt a very similar hotdog fold. HadA forms a tight dimer with HadB in which the proteins are sitting side-by-side, but are oriented anti-parallel. While HadB contributes the catalytically critical His-Asp dyad, HadA binds the fatty acid substrate in a long channel. The atypical double hotdog fold with a single active site formed by MtbHadAB gives rise to a long, narrow cavity that vertically traverses the fatty acid binding channel. At the base of this cavity lies Cys61, which upon mutation to Ser confers drug-resistance in TB patients. We show that inhibitors bind in this cavity and protrude into the substrate binding channel. Thus, inhibitors of MtbHadAB exert their effect by occluding substrate from the active site. The unveiling of this mechanism of inhibition paves the way for accelerating development of next generation of anti-TB drugs.