3SL2

ATP Forms a Stable Complex with the Essential Histidine Kinase WalK (YycG) Domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

ATP forms a stable complex with the essential histidine kinase WalK (YycG) domain.

Celikel, R.Veldore, V.H.Mathews, I.Devine, K.M.Varughese, K.I.

(2012) Acta Crystallogr D Biol Crystallogr 68: 839-845

  • DOI: 10.1107/S090744491201373X
  • Primary Citation of Related Structures:  
    3SL2

  • PubMed Abstract: 
  • In Bacillus subtilis, the WalRK (YycFG) two-component system coordinates murein synthesis with cell division. It regulates the expression of autolysins that function in cell-wall remodeling and of proteins that modulate autolysin activity. The transcription factor WalR is activated upon phosphorylation by the histidine kinase WalK, a multi-domain homodimer ...

    In Bacillus subtilis, the WalRK (YycFG) two-component system coordinates murein synthesis with cell division. It regulates the expression of autolysins that function in cell-wall remodeling and of proteins that modulate autolysin activity. The transcription factor WalR is activated upon phosphorylation by the histidine kinase WalK, a multi-domain homodimer. It autophosphorylates one of its histidine residues by transferring the γ-phosphate from ATP bound to its ATP-binding domain. Here, the high-resolution crystal structure of the ATP-binding domain of WalK in complex with ATP is presented at 1.61 Å resolution. The bound ATP remains intact in the crystal lattice. It appears that the strong binding interactions and the nature of the binding pocket contribute to its stability. The triphosphate moiety of ATP wraps around an Mg(2+) ion, providing three O atoms for coordination in a near-ideal octahedral geometry. The ATP molecule also makes strong interactions with the protein. In addition, there is a short contact between the exocyclic O3' of the sugar ring and O2B of the β-phosphate, implying an internal hydrogen bond. The stability of the WalK-ATP complex in the crystal lattice suggests that such a complex may exist in vivo poised for initiation of signal transmission. This feature may therefore be part of the sensing mechanism by which the WalRK two-component system is so rapidly activated when cells encounter conditions conducive for growth.


    Organizational Affiliation

    Department of Physiology and Biophysics, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, AR 72205, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Sensor histidine kinase yycGA177Bacillus subtilisMutation(s): 0 
Gene Names: yycGBSU40400
EC: 2.7.13.3
UniProt
Find proteins for Q45614 (Bacillus subtilis (strain 168))
Explore Q45614 
Go to UniProtKB:  Q45614
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ45614
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
D [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.04α = 90
b = 59.04β = 90
c = 99.31γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CNSrefinement
PROTEUM PLUSdata collection
XDSdata reduction
XDSdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-27
    Type: Initial release
  • Version 1.1: 2013-01-23
    Changes: Database references
  • Version 1.2: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.3: 2020-10-21
    Changes: Data collection, Database references, Derived calculations