5X1T

PpkA-294


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structures of the kinase domain of PpkA, a key regulatory component of T6SS, reveal a general inhibitory mechanism.

Li, P.P.Xu, D.Q.Ma, T.Q.Wang, D.Y.Li, W.D.He, J.H.Ran, T.T.Wang, W.W.

(2018) Biochem.J. 475: 2209-2224

  • DOI: 10.1042/BCJ20180077
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The type VI secretion system (T6SS) is a versatile and widespread export system found in many Gram-negative bacteria that delivers effector proteins into target cells. The functions of T6SSs are tightly regulated by diverse mechanisms at multiple lev ...

    The type VI secretion system (T6SS) is a versatile and widespread export system found in many Gram-negative bacteria that delivers effector proteins into target cells. The functions of T6SSs are tightly regulated by diverse mechanisms at multiple levels, including post-translational modification through threonine phosphorylation via the Ser/Thr protein kinase (STPK) PpkA. Here, we identified that PpkA is essential for T6SS secretion in Serratia marcescens since its deletion eliminated the secretion of haemolysin co-regulated protein, while the periplasmic and transmembrane portion of PpkA was found to be disposable for T6SS secretion. We further determined the crystal structure of the kinase domain of PpkA (PpkA-294). The structure of PpkA-294 was determined in its apo form to a 1.6 Å resolution as well as in complex with ATP to a 1.41 Å resolution and with an ATP analogue AMP-PCP to a 1.45 Å resolution. The residues in the activation loop of PpkA-294 were fully determined, and the N-terminus of the loop was folded into an unprecedented inhibitory helix, revealing that the PpkA kinase domain was in an auto-inhibitory state. The ternary MgATP-PpkA-294 complex was also inactive with nucleotide ribose and phosphates in unexpected and unproductive conformations. The αC-helix in the inactive PpkA-294 adopted a conformation towards the active site but with the conserved glutamate in the helix rotated away, which we suggest to be a general conformation for all STPK kinases in the inactive form. Structural comparison of PpkA with its eukaryotic homologues reinforced the universal regulation mechanism of protein kinases.


    Organizational Affiliation

    Shanghai Institute of Applied Physics, Chinese Academy of Sciences, 201204 Shanghai, PR China.,Institute of Agricultural Products Processing, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, PR China.,Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, PR China rant@njau.edu.cn wwwang@njau.edu.cn.,Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, PR China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PpkA-294
A
302Serratia sp. (strain FS14)Mutation(s): 0 
Find proteins for A0A1S4NYE5 (Serratia sp. (strain FS14))
Go to UniProtKB:  A0A1S4NYE5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.202 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 59.010α = 90.00
b = 65.560β = 90.00
c = 78.405γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Science Foundation of ChinaChina31400055
Natural Science Foundation of ChinaChina31170686
Natural Science Foundation of ChinaChina31100028
the Natural Science Foundation of Jiangsu ProvinceBK20140690
the Youth Science and Technology Innovation Fund from Nanjing Agricultural UniversityKJ2013027

Revision History 

  • Version 1.0: 2018-01-31
    Type: Initial release
  • Version 1.1: 2019-08-21
    Type: Data collection, Database references