5LNH

Structure of full length Unliganded CodY from Bacillus subtilis

Summary for 5LNH

• Entry DOI: 10.2210/pdb5lnh/pdb
• Related: 2B0L 2B18 2GX5 2HGV
• Descriptor: GTP-sensing transcriptional pleiotropic repressor CodY, SULFATE ION (3 entities in total)
• Functional Keywords: gaf, whth, transcriptional regulator, cody, transcription
• Biological source: Bacillus subtilis (strain 168)
• Cellular location: Cytoplasm: P39779
• Total number of polymer chains: 10
• Total formula weight: 300482.51

Authors

Wilkinson, A.J.,Levdikov, V.M.,Blagova, E.V. (deposition date: 2016-08-04, release date: 2017-01-11, Last modification date: 2024-01-10)

Primary citation

Levdikov, V.M.,Blagova, E.,Young, V.L.,Belitsky, B.R.,Lebedev, A.,Sonenshein, A.L.,Wilkinson, A.J.
Structure of the Branched-chain Amino Acid and GTP-sensing Global Regulator, CodY, from Bacillus subtilis.
J. Biol. Chem., 292:2714-2728, 2017

PubMed Abstract: CodY is a branched-chain amino acid (BCAA) and GTP sensor and a global regulator of transcription in low G + C Gram-positive bacteria. It controls the expression of over 100 genes and operons, principally by repressing during growth genes whose products are required for adaptations to nutrient limitation. However, the mechanism by which BCAA binding regulates transcriptional changes is not clear. It is known that CodY consists of a GAF (cMP-stimulated phosphodiesterases, denylate cyclases, hlA) domain that binds BCAAs and a winged helix-turn-helix (wHTH) domain that binds to DNA, but the way in which these domains interact and the structural basis of the BCAA dependence of this interaction are unknown. To gain new insights, we determined the crystal structure of unliganded CodY from revealing a 10-turn α-helix linking otherwise discrete GAF and wHTH domains. The structure of CodY in complex with isoleucine revealed a reorganized GAF domain. In both complexes CodY was tetrameric. Size exclusion chromatography with multiangle laser light scattering (SEC-MALLS) experiments showed that CodY is a dimer at concentrations found in bacterial cells. Comparison of structures of dimers of unliganded CodY and CodY-Ile derived from the tetramers showed a splaying of the wHTH domains when Ile was bound; splaying is likely to account for the increased affinity of Ile-bound CodY for DNA. Electrophoretic mobility shift and SEC-MALLS analyses of CodY binding to 19-36-bp operator fragments are consistent with isoleucine-dependent binding of two CodY dimers per duplex. The implications of these observations for effector control of CodY activity are discussed.

PubMed: 28011634
DOI: 10.1074/jbc.M116.754309

Experimental method

X-RAY DIFFRACTION (3 Å)