Biological Assembly 1  

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 30637.18 
• Atom Count: 2048 
• Residue Count: 283 
• Unique protein chains: 1

4OW8

Crystal structure of kinase domain of PknA from Mtb

• DOI: 10.2210/pdb4OW8/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2014-01-31 Released: 2015-02-04 
• Deposition Author(s): Ravala, S.K., Singh, S., Yadav, G.S., Karthikeyan, S., Chakraborti, P.K.
• Funding Organization(s): CSIR 

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Experimental Data Snapshot

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

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

• PubMed: 25665034 
• DOI: 10.1111/febs.13230


• 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. 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.

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Organizational Affiliation: 

CSIR-Institute of Microbial Technology, Chandigarh, India.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Serine/threonine-protein kinase PknA	A	283	Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)	Mutation(s): 0  Gene Names: pknA EC: 2.7.11.1
Find proteins for P9WI82 (Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)) Go to UniProtKB:  P9WI82

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.275 
• R-Value Work: 0.226 
• Space Group: I 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 54.139	α = 90.00
b = 58.412	β = 96.20
c = 78.867	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data scaling
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2014-01-31 
• Released Date: 2015-02-04 
• Deposition Author(s): Ravala, S.K., Singh, S., Yadav, G.S., Karthikeyan, S., Chakraborti, P.K.

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Funding Organization	Location	Grant Number
CSIR	India	--

Revision History 

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