4U7O

Active histidine kinase bound with ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Conformational dynamics of the essential sensor histidine kinase WalK.

Cai, Y.Su, M.Ahmad, A.Hu, X.Sang, J.Kong, L.Chen, X.Wang, C.Shuai, J.Han, A.

(2017) Acta Crystallogr D Struct Biol 73: 793-803

  • DOI: 10.1107/S2059798317013043
  • Primary Citation of Related Structures:  
    4U7N, 4U7O, 5C93, 4ZKI

  • PubMed Abstract: 
  • Two-component systems (TCSs) are key elements in bacterial signal transduction in response to environmental stresses. TCSs generally consist of sensor histidine kinases (SKs) and their cognate response regulators (RRs). Many SKs exhibit autokinase, phosphoryltransferase and phosphatase activities, which regulate RR activity through a phosphorylation and dephosphorylation cycle ...

    Two-component systems (TCSs) are key elements in bacterial signal transduction in response to environmental stresses. TCSs generally consist of sensor histidine kinases (SKs) and their cognate response regulators (RRs). Many SKs exhibit autokinase, phosphoryltransferase and phosphatase activities, which regulate RR activity through a phosphorylation and dephosphorylation cycle. However, how SKs perform different enzymatic activities is poorly understood. Here, several crystal structures of the minimal catalytic region of WalK, an essential SK from Lactobacillus plantarum that shares 60% sequence identity with its homologue VicK from Streptococcus mutans, are presented. WalK adopts an asymmetrical closed structure in the presence of ATP or ADP, in which one of the CA domains is positioned close to the DHp domain, thus leading both the β- and γ-phosphates of ATP/ADP to form hydrogen bonds to the ℇ- but not the δ-nitrogen of the phosphorylatable histidine in the DHp domain. In addition, the DHp domain in the ATP/ADP-bound state has a 25.7° asymmetrical helical bending coordinated with the repositioning of the CA domain; these processes are mutually exclusive and alternate in response to helicity changes that are possibly regulated by upstream signals. In the absence of ATP or ADP, however, WalK adopts a completely symmetric open structure with its DHp domain centred between two outward-reaching CA domains. In summary, these structures of WalK reveal the intrinsic dynamic properties of an SK structure as a molecular basis for multifunctionality.


    Organizational Affiliation

    State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiang'an, Xiamen 361102, People's Republic of China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histidine protein kinase sensor proteinA, B277Lacticaseibacillus plantarum JDM1Mutation(s): 0 
Gene Names: hpk1JDM1_0052
UniProt
Find proteins for A0A0M3KKX3 (Lactobacillus plantarum (strain JDM1))
Explore A0A0M3KKX3 
Go to UniProtKB:  A0A0M3KKX3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AN2 (Subject of Investigation/LOI)
Query on AN2

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]AMP PHOSPHORAMIDATE
C10 H16 N6 O9 P2
FQMDCEJHLOLKLI-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.528α = 90
b = 98.389β = 90
c = 116.369γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2014-07-31 
  • Released Date: 2015-09-02 
  • Deposition Author(s): Cai, Y., Hu, X., Sang, J.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina--

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-02
    Type: Initial release
  • Version 1.1: 2017-10-18
    Changes: Author supporting evidence, Derived calculations
  • Version 1.2: 2017-10-25
    Changes: Database references