7NAA

Crystal structure of Mycobacterium tuberculosis H37Rv PknF kinase domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure of the Mycobacterium tuberculosis c PknF and conformational changes induced in forkhead-associated regulatory domains.

Cabarca, S.Frazao de Souza, M.Albert de Oliveira, A.Vignoli Muniz, G.S.Lamy, M.T.Vinicius Dos Reis, C.Takarada, J.Effer, B.Souza, L.S.Iriarte de la Torre, L.Counago, R.Pinto Oliveira, C.L.Balan, A.

(2021) Curr Res Struct Biol 3: 165-178

  • DOI: https://doi.org/10.1016/j.crstbi.2021.07.001
  • Primary Citation of Related Structures:  
    7NAA

  • PubMed Abstract: 

    Mycobacterium tuberculosis ( Mtb ) has 11 Serine-Threonine Protein Kinases (STPK) that control numerous physiological processes, including cell growth, cell division, metabolic flow, and transcription. PknF is one of the 11 Mtb STPKs that has, among other substrates, two FHA domains (FHA-1 and FHA-2) of the ATP-Binding Cassette (ABC) transporter Rv1747. Phosphorylation in T152 and T210 located in a non-structured linker that connects Rv1747 FHA domains is considerate to be the regulatory mechanism of the transporter. In this work, we resolved the three-dimensional structure of the PknF catalytic domain (cPknF) in complex with the human kinase inhibitor IKK16. cPknF is conserved when compared to other STPKs but shows specific residues in the binding site where the inhibitor is positioned. In addition, using Small Angle X-Ray Scattering analysis we monitored the behavior of the wild type and three FHA-phosphomimetic mutants in solution, and measured the cPknF affinity for these domains. The kinase showed higher affinity for the non-phosphorylated wild type domain and preference for phosphorylation of T152 inducing the rapprochement of the domains and significant structural changes. The results shed some light on the process of regulating the transporter's activity by phosphorylation and arises important questions about evolution and importance of this mechanism for the bacillus.


  • Organizational Affiliation

    Programa de Pós-graduação em Genética, Universidade Estadual de Campinas, Campinas, 13083-862, SP, Brazil.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Non-specific serine/threonine protein kinase
A, B, C, D
278Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
EC: 2.7.11.1
UniProt
Find proteins for P9WI75 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WI75 
Go to UniProtKB:  P9WI75
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WI75
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.127α = 90
b = 239.33β = 90
c = 53.982γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil2016/20182-9
Brazilian National Council for Scientific and Technological Development (CNPq)Brazil401505/2016-2

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-04
    Type: Initial release
  • Version 1.1: 2021-08-25
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description