3T8Y | pdb_00003t8y

Crystal structure of the response regulator domain of Thermotoga maritima CheB

• PDB DOI: https://doi.org/10.2210/pdb3T8Y/pdb

• Classification: HYDROLASE
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-08-02 Released: 2011-09-14 
• Deposition Author(s): Park, S.Y., Crane, B.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.245 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.234 (DCC) 

Literature

Structural insight into the low affinity between Thermotoga maritima CheA and CheB compared to their Escherichia coli/Salmonella typhimurium counterparts

Park, S.Y., Crane, B.R.

(2011) Int J Biol Macromol 49: 794-800

• PubMed: 21816169 
• DOI: https://doi.org/10.1016/j.ijbiomac.2011.07.012
• Primary Citation Related Structures: 
  3T8Y


• PubMed Abstract: 
  

  CheA-mediated CheB phosphorylation and the subsequent CheB-mediated demethylation of the chemoreceptors are important steps required for the bacterial chemotactic adaptation response. Although Escherichia coli CheB has been reported to interact with CheA competitively against CheY, we have observed that Thermotoga maritima CheB has no detectable CheA-binding. By determining the CheY-like domain crystal structure of T. maritima CheB, and comparing against the T. maritima CheY and Salmonella typhimurium CheB structures, we propose that the two consecutive glutamates in the β4/α4 loop of T. maritima CheB that is absent in T. maritima CheY and in E. coli/S. typhimurium CheB may be one factor contributing to the low CheA affinity.

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Organizational Affiliation: 
• School of Systems Biomedical Science, College of Natural Sciences, Soongsil University, Seoul, Republic of Korea. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.78 kDa 
• Atom Count: 2,297 
• Modeled Residue Count: 272 
• Deposited Residue Count: 328 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chemotaxis response regulator protein-glutamate methylesterase	A, B	164	Thermotoga maritima	Mutation(s): 0  Gene Names: cheB EC: 3.1.1.61 (PDB Primary Data), 3.5.1.44 (UniProt)
UniProt
Find proteins for Q9WYN9 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WYN9  Go to UniProtKB:  Q9WYN9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PB	C [auth A], D [auth B]	LEAD (II) ION Pb RVPVRDXYQKGNMQ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.245 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.234 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.715	α = 90
b = 53.679	β = 90
c = 131.565	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-14 
Deposition Author(s): Park, S.Y., Crane, B.R.

Revision History  

• Version 1.0: 2011-09-14
  Type: Initial release
  
• Version 1.1: 2013-06-19
  Changes: Database references
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations