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1  structure 2  species 0  interactions 2  sequences 1  architecture

Family: CnrY (PF17524)

Summary: anti-sigma factor CnrY

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anti-sigma factor CnrY Provide feedback

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 [1]. 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-σ 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 [2].

Literature references

  1. Paget MS;, Biomolecules. 2015;5:1245-1265.: Bacterial Sigma Factors and Anti-Sigma Factors: Structure, Function and Distribution. PUBMED:26131973 EPMC:26131973

  2. Maillard AP, Girard E, Ziani W, Petit-Hartlein I, Kahn R, Coves J;, J Mol Biol. 2014;426:2313-2327.: The crystal structure of the anti-sigma factor CnrY in complex with the sigma factor CnrH shows a new structural class of anti-sigma factors targeting extracytoplasmic function sigma factors. PUBMED:24727125 EPMC:24727125


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Domain organisation

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Alignments

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Representative proteomes UniProt
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NCBI
(17)
Meta
(0)
RP15
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RP35
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RP55
(2)
RP75
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  Seed
(2)
Full
(2)
Representative proteomes UniProt
(11)
NCBI
(17)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(2)
RP75
(6)
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Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

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This family is new in this Pfam release.

Seed source: PRODOM:PD065580
Previous IDs: none
Type: Family
Author: El-Gebali S
Number in seed: 2
Number in full: 2
Average length of the domain: 94.50 aa
Average identity of full alignment: 38 %
Average coverage of the sequence by the domain: 100.00 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 29.9 155.1
Noise cut-off 24.6 19.2
Model length: 95
Family (HMM) version: 1
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Species distribution

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the CnrY domain has been found. There are 1 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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