4X3F

Crystal structure of the intracellular domain of the M. tuberculosis Ser/Thr kinase PknA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The crystal structure of the catalytic domain of the ser/thr kinase PknA from M. tuberculosis shows an Src-like autoinhibited conformation.

Wagner, T.Alexandre, M.Duran, R.Barilone, N.Wehenkel, A.Alzari, P.M.Bellinzoni, M.

(2015) Proteins 83: 982-988

  • DOI: https://doi.org/10.1002/prot.24754
  • Primary Citation of Related Structures:  
    4X3F

  • PubMed Abstract: 

    Signal transduction mediated by Ser/Thr phosphorylation in Mycobacterium tuberculosis has been intensively studied in the last years, as its genome harbors eleven genes coding for eukaryotic-like Ser/Thr kinases. Here we describe the crystal structure and the autophosphorylation sites of the catalytic domain of PknA, one of two protein kinases essential for pathogen's survival. The structure of the ligand-free kinase domain shows an auto-inhibited conformation similar to that observed in human Tyr kinases of the Src-family. These results reinforce the high conservation of structural hallmarks and regulation mechanisms between prokaryotic and eukaryotic protein kinases.


  • Organizational Affiliation

    Institut Pasteur, Unité De Microbiologie Structurale, Paris, 75724, France; CNRS UMR 3528, Paris, 75724, France; Université Paris Diderot, Sorbonne Paris Cité, Microbiologie Structurale, Paris, 75724, France.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PknA337Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: pknARv0015cMTCY10H4.15c
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
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PknA337Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: pknARv0015cMTCY10H4.15c
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
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PknA337Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: pknARv0015cMTCY10H4.15c
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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.220 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.31α = 90
b = 150.18β = 96.98
c = 96.54γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-21
    Type: Initial release
  • Version 1.1: 2015-04-22
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description