Conserved Protein Domain Family

cl38795: CnrY Superfamily 
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anti-sigma factor CnrY
This family is found in alpha and beta proteobacteria. Family members include anti-sigma factor CnrY from Cupriavidus metallidurans. Sigma factors are multi-domain sub-units of bacterial RNA polymerase (RNAP) that play critical roles in transcription initiation, including the recognition and opening of promoters as well as the initial steps in RNA synthesis. They also control a wide variety of adaptive responses such as morphological development and the management of stress. A recurring theme in sigma factor control is their sequestration by anti-sigma factors that occlude their RNAP-binding determinants. CnrH, controls cobalt and nickel resistance in Cupriavidus metallidurans. CnrH is regulated by a complex of two transmembrane proteins: the periplasmic sensor CnrX and the anti-sigma CnrY. At rest, CnrH is sequestered by CnrY whose 45-residue-long cytosolic domain is one of the shortest anti-sigma domains. Upon Ni(II) or Co(II) ions detection by CnrX in the periplasm, CnrH is released between CnrH and the cytosolic domain of CnrY (CnrYc). The CnrH/CnrYC complex displays an unexpected structural similarity to the anti-sigma NepR in complex with its antagonist PhyR, whereas NepR shares no sequence similarity with CnrY. Crystal structure of CnrH/CnrY shows that CnrYC residues 3-19 are folded as a well-defined alpha-helix. The peptide further extends along the hydrophobic groove of sigma 2 with no canonical structure except for a short helical turn spanning residues 24-28. CnrY has a hydrophobic knob made of V4, W7 and L8 side chains protruding into sigma 4 hydrophobic pocket and contributing to the interface. In vivo investigation of CnrY function pinpoints part of the hydrophobic knob as a hotspot in CnrH inhibitory binding.
Accession: cl38795
PSSM Id: 422937
Name: CnrY
Created: 19-Sep-2018
Updated: 24-Nov-2020
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