6YMZ

Structure of the CheB methylsterase from P. atrosepticum SCRI1043


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Evidence for Pentapeptide-Dependent and Independent CheB Methylesterases.

Velando, F.Gavira, J.A.Rico-Jimenez, M.Matilla, M.A.Krell, T.

(2020) Int J Mol Sci 21

  • DOI: 10.3390/ijms21228459
  • Primary Citation of Related Structures:  
    6YMZ

  • PubMed Abstract: 
  • Many bacteria possess multiple chemosensory pathways that are composed of homologous signaling proteins. These pathways appear to be functionally insulated from each other, but little information is available on the corresponding molecular basis. We report here a novel mechanism that contributes to pathway insulation ...

    Many bacteria possess multiple chemosensory pathways that are composed of homologous signaling proteins. These pathways appear to be functionally insulated from each other, but little information is available on the corresponding molecular basis. We report here a novel mechanism that contributes to pathway insulation. We show that, of the four CheB paralogs of Pseudomonas aeruginosa PAO1, only CheB 2 recognizes a pentapeptide at the C-terminal extension of the McpB (Aer2) chemoreceptor ( K D = 93 µM). McpB is the sole chemoreceptor that stimulates the Che2 pathway, and CheB 2 is the methylesterase of this pathway. Pectobacterium atrosepticum SCRI1043 has a single CheB, CheB_Pec, and 19 of its 36 chemoreceptors contain a C-terminal pentapeptide. The deletion of cheB_Pec abolished chemotaxis, but, surprisingly, none of the pentapeptides bound to CheB_Pec. To determine the corresponding structural basis, we solved the 3D structure of CheB_Pec. Its structure aligned well with that of the pentapeptide-dependent enzyme from Salmonella enterica . However, no electron density was observed in the CheB_Pec region corresponding to the pentapeptide-binding site in the Escherichia coli CheB. We hypothesize that this structural disorder is associated with the failure to bind pentapeptides. Combined data show that CheB methylesterases can be divided into pentapeptide-dependent and independent enzymes.


    Organizational Affiliation

    Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein-glutamate methylesterase/protein-glutamine glutaminaseA, B, C, D, E356Pectobacterium atrosepticum SCRI1043Mutation(s): 0 
Gene Names: cheBECA1693
EC: 3.1.1.61 (PDB Primary Data), 3.5.1.44 (PDB Primary Data)
Find proteins for Q6D6I7 (Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672))
Explore Q6D6I7 
Go to UniProtKB:  Q6D6I7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
T [auth E]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A], J [auth A], M [auth C], P [auth C], R [auth D], U [auth E], V [auth E]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
F [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
G [auth A], I [auth A], K [auth B], L [auth B], N [auth C], O [auth C], Q [auth D], S [auth E]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.741α = 90
b = 148.741β = 90
c = 206.34γ = 90
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainBIO2013-4297-P
Spanish Ministry of Science, Innovation, and UniversitiesSpainBIO2016-74875-P

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-17
    Type: Initial release