title: Crystal Structure of Mycobacterium tuberculosis H37Rv AldR (Rv2779c), a Regulator of the ald Gene: DNA BINDING AND IDENTIFICATION OF SMALL MOLECULE INHIBITORS.
abstract: Here we report the crystal structure of M. tuberculosis AldR (Rv2779c) showing that the N-terminal DNA-binding domains are swapped, forming a dimer, and four dimers are assembled into an octamer through crystal symmetry. The C-terminal domain is involved in oligomeric interactions that stabilize the oligomer, and it contains the effector-binding sites. The latter sites are 30-60% larger compared with homologs like MtbFFRP (Rv3291c) and can consequently accommodate larger molecules. MtbAldR binds to the region upstream to the ald gene that is highly up-regulated in nutrient-starved tuberculosis models and codes for l-alanine dehydrogenase (MtbAld; Rv2780). Further, the MtbAldR-DNA complex is inhibited upon binding of Ala, Tyr, Trp and Asp to the protein. Studies involving a ligand-binding site G131T mutant show that the mutant forms a DNA complex that cannot be inhibited by adding the amino acids. Comparative studies suggest that binding of the amino acids changes the relative spatial disposition of the DNA-binding domains and thereby disrupt the protein-DNA complex. Finally, we identified small molecules, including a tetrahydroquinoline carbonitrile derivative (S010-0261), that inhibit the MtbAldR-DNA complex. The latter molecules represent the very first inhibitors of a feast/famine regulatory protein from any source and set the stage for exploring MtbAldR as a potential anti-tuberculosis target.
authors.affiliation: From the Molecular and Structural Biology Division and.
authors.forename: Abhishek
authors.initials: A
authors.lastname: Dey
authors.affiliation: From the Molecular and Structural Biology Division and.
authors.forename: Sonal
authors.initials: S
authors.lastname: Shree
authors.affiliation: the Medicinal and Process Chemistry Division, Council of Scientific and Industrial Research-Central Drug Research Institute, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh 226031, India.
authors.forename: Sarvesh Kumar
authors.initials: SK
authors.lastname: Pandey
authors.affiliation: the Medicinal and Process Chemistry Division, Council of Scientific and Industrial Research-Central Drug Research Institute, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh 226031, India.
authors.forename: Rama Pati
authors.initials: RP
authors.lastname: Tripathi
authors.affiliation: From the Molecular and Structural Biology Division and r_ravishankar@cdri.res.in.
authors.forename: Ravishankar
authors.initials: R
authors.lastname: Ramachandran
mesh_terms: D050788:Alanine Dehydrogenase / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D000596:Amino Acids / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D001665:Binding Sites / Q000235:genetics; D002942:Circular Dichroism; D018360:Crystallography, X-Ray; D015964:Gene Expression Regulation, Bacterial / Q000187:drug effects / Q000235:genetics*; D008958:Models, Molecular; D009169:Mycobacterium tuberculosis / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D000072417:Protein Domains; D017433:Protein Structure, Secondary; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics; D054852:Small Molecule Libraries / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism
chemical_list: D000596:Amino Acids; D001426:Bacterial Proteins; D054852:Small Molecule Libraries; D014157:Transcription Factors; D050788:Alanine Dehydrogenase
keywords: AldR; DNA binding protein; DNA-protein interaction; Lrp/Asnc; Mycobacterium tuberculosis; crystal structure; enzyme inhibitor; feast/famine regulatory proteins; oligomeric association; regulator