4OW8

Crystal structure of kinase domain of PknA from Mtb


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Evidence that phosphorylation of threonine in the GT motif triggers activation of PknA, a eukaryotic-type serine/threonine kinase from Mycobacterium tuberculosis.

Ravala, S.K.Singh, S.Yadav, G.S.Kumar, S.Karthikeyan, S.Chakraborti, P.K.

(2015) FEBS J 282: 1419-1431

  • DOI: 10.1111/febs.13230
  • Primary Citation of Related Structures:  
    4OW8

  • PubMed Abstract: 
  • Phosphorylation of the activation loop in the catalytic domain of the RD family of bacterial eukaryotic-type Ser/Thr protein kinases (STPK) induces their conformational transition from an inactive to active state. However, mechanistic insights into the phosphorylation-mediated transition of these STPKs from an inactive to active state remain unknown ...

    Phosphorylation of the activation loop in the catalytic domain of the RD family of bacterial eukaryotic-type Ser/Thr protein kinases (STPK) induces their conformational transition from an inactive to active state. However, mechanistic insights into the phosphorylation-mediated transition of these STPKs from an inactive to active state remain unknown. In the present study, we addressed this issue with PknA, an essential STPK from Mycobacterium tuberculosis. We found that the catalytic activity of PknA is confined within the N-terminal 283 amino acids (PknA-283). The crystal structure of PknA-283 in unphosphorylated form showed an ordered activation loop and existed in an inactive state preventing the phosphorylation of its cognate substrate(s). Peptide mass finger printing studies revealed that all activation loop threonines (Thr172, Thr174 and Thr180) were phosphorylated in the activated PknA-283 protein. Substitution of Thr180 with Ala/Asp (T180A/T180D) resulted in catalytically defective mutants, whereas a double mutant replacing Thr172 and Thr174 with Ala (T172A-T174A) was deficient in kinase activity. Analysis of PknA-283 structure, together with biochemical studies, revealed the possibility of phosphorylation of Thr180 via a cis mechanism, whereas that of Thr172 and Thr174 occurs via a trans mechanism. Moreover, unlike wild-type, these mutants did not show any drastic change in cell morphology in a phenotypic assay, implicating the role of all threonines in the activation loop towards the functionality of PknA. Thus, our findings offer a model for kinase activation showing that the phosphorylation of Thr180 triggers PknA to transphosphorylate Thr172/Thr174, thereby governing its functionality.


    Organizational Affiliation

    CSIR-Institute of Microbial Technology, Chandigarh, India.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PknAA283Mycobacterium tuberculosisMutation(s): 0 
Gene Names: MT0018MTCY10H4.15cRv0015cpknA
EC: 2.7.11.1
UniProt
Find proteins for P9WI83 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WI83 
Go to UniProtKB:  P9WI83
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WI83
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.139α = 90
b = 58.412β = 96.2
c = 78.867γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
REFMACrefinement
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
CSIRIndia--

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-04
    Type: Initial release
  • Version 1.1: 2015-02-25
    Changes: Database references
  • Version 1.2: 2015-03-04
    Changes: Database references
  • Version 1.3: 2015-03-11
    Changes: Database references
  • Version 1.4: 2015-04-22
    Changes: Database references
  • Version 1.5: 2017-11-22
    Changes: Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary