The crystal structure of Histidine Kinase YycG with ADP

Experimental Data Snapshot

  • Resolution: 3.40 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


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: https://doi.org/10.1107/S2059798317013043
  • Primary Citation of Related Structures:  
    4U7N, 4U7O, 4ZKI, 5C93

  • 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. 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

    Department of Physics, Xiamen University, Xiang'an, Xiamen 361102, People's Republic of China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histidine kinase
A, B
277Lactiplantibacillus plantarum JDM1Mutation(s): 0 
Gene Names: hpk1JDM1_0052
Find proteins for A0A0M3KKX3 (Lactiplantibacillus plantarum (strain JDM1))
Explore A0A0M3KKX3 
Go to UniProtKB:  A0A0M3KKX3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0M3KKX3
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ADP

Download Ideal Coordinates CCD File 
C10 H15 N5 O10 P2
Experimental Data & Validation

Experimental Data

  • Resolution: 3.40 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.499α = 90
b = 96.034β = 90
c = 119.351γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

  • Released Date: 2016-05-04 
  • Deposition Author(s): Cai, Y.

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)China--

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2017-10-04
    Changes: Data collection, Derived calculations
  • Version 1.2: 2017-10-25
    Changes: Database references
  • Version 1.3: 2022-03-23
    Changes: Author supporting evidence, Database references
  • Version 1.4: 2023-11-08
    Changes: Data collection, Refinement description