3A0V | pdb_00003a0v

PAS domain of histidine kinase ThkA (TM1359) (SeMet, F486M/F489M)

• PDB DOI: https://doi.org/10.2210/pdb3A0V/pdb

• Classification: TRANSFERASE
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2009-03-24 Released: 2009-10-20 
• Deposition Author(s): Yamada, S., Sugimoto, H., Kobayashi, M., Ohno, A., Nakamura, H., Shiro, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.258 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Literature

Structure of PAS-linked histidine kinase and the response regulator complex

Yamada, S., Sugimoto, H., Kobayashi, M., Ohno, A., Nakamura, H., Shiro, Y.

(2009) Structure 17: 1333-1344

• PubMed: 19836334 
• DOI: https://doi.org/10.1016/j.str.2009.07.016
• Primary Citation Related Structures: 
  3A0R, 3A0S, 3A0T, 3A0U, 3A0V, 3A0W, 3A0X, 3A0Y, 3A0Z, 3A10


• PubMed Abstract: 
  

  We determined the structure of the complex of the sensory histidine kinase (HK) and its cognate response regulator (RR) in the two-component signal transduction system of Thermotoga maritima. This was accomplished by fitting the high-resolution structures of the isolated HK domains and the RR onto the electron density map (3.8 A resolution) of the HK/RR complex crystal. Based on the structural information, we evaluated the roles of both interdomain and intermolecular interactions in the signal transduction of the cytosolic PAS-linked HK and RR system, in particular the O(2)-sensor FixL/FixJ system. The PAS-sensor domain of HK interacts with the catalytic domain of the same polypeptide chain by creating an interdomain beta sheet. The interaction site between HK and RR, which was confirmed by NMR, is suitable for the intermolecular transfer reaction of the phosphoryl group, indicating that the observed interaction is important for the phosphatase activity of HK that dephosphorylates phospho-RR.

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Organizational Affiliation: 
• RIKEN SPring-8 Center, Kouto 1-1-1, Sayo, Hyogo, Japan.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 11.51 kDa 
• Atom Count: 913 
• Modeled Residue Count: 96 
• Deposited Residue Count: 96 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sensor protein	A	96	Thermotoga maritima	Mutation(s): 2  Gene Names: TM_1359 EC: 2.7.13.3
UniProt
Find proteins for Q9X180 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X180  Go to UniProtKB:  Q9X180

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EOH	B [auth A], C [auth A], D [auth A], E [auth A]	ETHANOL C2 H6 O LFQSCWFLJHTTHZ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.258 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.238	α = 90
b = 43.238	β = 90
c = 116.16	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-20 
Deposition Author(s): Yamada, S., Sugimoto, H., Kobayashi, M., Ohno, A., Nakamura, H., Shiro, Y.

Revision History  

• Version 1.0: 2009-10-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.3: 2024-10-30
  Changes: Data collection, Structure summary