7W0W

The novel membrane-proximal sensing mechanism in a broad-ligand binding chemoreceptor McpA of Bacillus velezensis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.182 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Signal binding at both modules of its dCache domain enables the McpA chemoreceptor of Bacillus velezensis to sense different ligands.

Feng, H.Lv, Y.Krell, T.Fu, R.Liu, Y.Xu, Z.Du, W.Shen, Q.Zhang, N.Zhang, R.

(2022) Proc Natl Acad Sci U S A 119: e2201747119-e2201747119

  • DOI: https://doi.org/10.1073/pnas.2201747119
  • Primary Citation of Related Structures:  
    7W0W

  • PubMed Abstract: 

    Bacteria have evolved multiple signal transduction systems that permit an adaptation to changing environmental conditions. Chemoreceptor-based signaling cascades are very abundant in bacteria and are among the most complex signaling systems. Currently, our knowledge on the molecular features that determine signal recognition at chemoreceptors is limited. Chemoreceptor McpA of Bacillus velezensis SQR9 has been shown to mediate chemotaxis to a broad range of different ligands. Here we show that its ligand binding domain binds directly 13 chemoattractants. We provide support that organic acids and amino acids bind to the membrane-distal and membrane-proximal module of the dCache domain, respectively, whereas binding of sugars/sugar alcohols occurred at both modules. Structural biology studies combined with site-directed mutagenesis experiments have permitted to identify 10 amino acid residues that play key roles in the recognition of multiple ligands. Residues in membrane-distal and membrane-proximal regions were central for sensing organic acids and amimo acids, respectively, whereas all residues participated in sugars/sugar alcohol sensing. Most characterized chemoreceptors possess a narrow and well-defined ligand spectrum. We propose here a sensing mechanism involving both dCache modules that allows the integration of very diverse signals by a single chemoreceptor.


  • Organizational Affiliation

    Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, The Key Laboratory of Plant Immunity, Nanjing Agricultural University, 210095 Nanjing, People's Republic of China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methyl-accepting chemotaxis protein
A, B
205Bacillus velezensisMutation(s): 0 
Gene Names: IPZ53_14355JKJ03_14450
UniProt
Find proteins for A7Z835 (Bacillus velezensis (strain DSM 23117 / BGSC 10A6 / LMG 26770 / FZB42))
Explore A7Z835 
Go to UniProtKB:  A7Z835
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7Z835
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LMR
Query on LMR

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
(2S)-2-hydroxybutanedioic acid
C4 H6 O5
BJEPYKJPYRNKOW-REOHCLBHSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
F [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO

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D [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.182 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 180.161α = 90
b = 32.855β = 90
c = 57.903γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)31900080
Other government2019M651847

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-06
    Type: Initial release
  • Version 1.1: 2023-01-18
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description