PDBsum entry 5k7h

Transcription

PDB id: 5k7h

Contents

Protein chains

184 a.a.

Ligands

IVC ×2

Metals

_NI

_CL ×4

Waters ×28

References listed in PDB file

Key reference

• Title: The aibr-Isovaleryl coenzyme a regulator and its DNA binding site - A model for the regulation of alternative de novo isovaleryl coenzyme a biosynthesis in myxococcus xanthus.
• Authors: T.Bock, C.Volz, V.Hering, A.Scrima, R.Müller, W.Blankenfeldt.
• Ref.: Nucleic Acids Res, 2017, 45, 2166-2178.
• PubMed id: 27940564

Abstract

Isovaleryl coenzyme A (IV-CoA) is an important building block of iso-fatty acids. In myxobacteria, IV-CoA is essential for the formation of signaling molecules involved in fruiting body formation. Leucine degradation is the common source of IV-CoA, but a second, de novo biosynthetic route to IV-CoA termed AIB (alternative IV-CoA biosynthesis) was recently discovered in M. xanthus. The AIB-operon contains the TetR-like transcriptional regulator AibR, which we characterize in this study. We demonstrate that IV-CoA binds AibR with micromolar affinity and show by gelshift experiments that AibR interacts with the promoter region of the AIB-operon once IV-CoA is present. We identify an 18-bp near-perfect palindromic repeat as containing the AibR operator and provide evidence that AibR also controls an additional genomic locus coding for a putative acetyl-CoA acetyltransferase. To elucidate atomic details, we determined crystal structures of AibR in the apo, the IV-CoA- and the IV-CoA-DNA-bound state to 1.7 Å, 2.35 Å and 2.92 Å, respectively. IV-CoA induces partial unfolding of an α-helix, which allows sequence-specific interactions between AibR and its operator. This study provides insights into AibR-mediated regulation and shows that AibR functions in an unusual TetR-like manner by blocking transcription not in the ligand-free but in the effector-bound state.