PDBsum entry 5eb2

Transcription

PDB id: 5eb2

Contents

Protein chains

153 a.a.

Ligands

TRP

SO4 ×2

Waters ×98

PDB id:

5eb2

Name:

Transcription

Title:

Trp-bound yfir

Structure:

Yfir. Chain: a, b. Fragment: unp residues 35-190. Engineered: yes

Source:

Pseudomonas aeruginosa pao1. Organism_taxid: 208964. Strain: pao1. Gene: yfir, pa1121. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.71Å R-factor: 0.197 R-free: 0.230

Authors:

M.Xu,X.Yang,X.-A.Yang,L.Zhou,T.-Z.Liu,Z.Fan,T.Jiang

Key ref:

M.Xu et al. (2016). Structural insights into the regulatory mechanism of the Pseudomonas aeruginosa YfiBNR system. Protein Cell, 7, 403-416. PubMed id: 27113583 DOI: 10.1007/s13238-016-0264-7

Date:

17-Oct-15 Release date: 18-May-16

Protein chains

Q9I4L4  (Q9I4L4_PSEAE) -  Negative regulator YfiR from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)

Seq: 190 a.a.

Struc: 153 a.a.

DOI no: 10.1007/s13238-016-0264-7

Protein Cell 7:403-416 (2016)

PubMed id: 27113583

Structural insights into the regulatory mechanism of the Pseudomonas aeruginosa YfiBNR system.

M.Xu, X.Yang, X.A.Yang, L.Zhou, T.Z.Liu, Z.Fan, T.Jiang.

ABSTRACT

YfiBNR is a recently identified bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) signaling system in opportunistic pathogens. It is a key regulator of biofilm formation, which is correlated with prolonged persistence of infection and antibiotic drug resistance. In response to cell stress, YfiB in the outer membrane can sequester the periplasmic protein YfiR, releasing its inhibition of YfiN on the inner membrane and thus provoking the diguanylate cyclase activity of YfiN to induce c-di-GMP production. However, the detailed regulatory mechanism remains elusive. Here, we report the crystal structures of YfiB alone and of an active mutant YfiB(L43P) complexed with YfiR with 2:2 stoichiometry. Structural analyses revealed that in contrast to the compact conformation of the dimeric YfiB alone, YfiB(L43P) adopts a stretched conformation allowing activated YfiB to penetrate the peptidoglycan (PG) layer and access YfiR. YfiB(L43P) shows a more compact PG-binding pocket and much higher PG binding affinity than wild-type YfiB, suggesting a tight correlation between PG binding and YfiB activation. In addition, our crystallographic analyses revealed that YfiR binds Vitamin B6 (VB6) or L-Trp at a YfiB-binding site and that both VB6 and L-Trp are able to reduce YfiB(L43P)-induced biofilm formation. Based on the structural and biochemical data, we propose an updated regulatory model of the YfiBNR system.