5CKL

Fic protein from Neisseria meningitidis (NmFic) mutant E156R in dimeric form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.99 Å
  • R-Value Free: 0.125 
  • R-Value Work: 0.112 
  • R-Value Observed: 0.113 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Intrinsic regulation of FIC-domain AMP-transferases by oligomerization and automodification.

Stanger, F.V.Burmann, B.M.Harms, A.Aragao, H.Mazur, A.Sharpe, T.Dehio, C.Hiller, S.Schirmer, T.

(2016) Proc Natl Acad Sci U S A 113: E529-E537

  • DOI: 10.1073/pnas.1516930113
  • Primary Citation of Related Structures:  
    5CGL, 5CKL, 5CMT

  • PubMed Abstract: 
  • Filamentation induced by cyclic AMP (FIC)-domain enzymes catalyze adenylylation or other posttranslational modifications of target proteins to control their function. Recently, we have shown that Fic enzymes are autoinhibited by an α-helix (αinh) that partly obstructs the active site ...

    Filamentation induced by cyclic AMP (FIC)-domain enzymes catalyze adenylylation or other posttranslational modifications of target proteins to control their function. Recently, we have shown that Fic enzymes are autoinhibited by an α-helix (αinh) that partly obstructs the active site. For the single-domain class III Fic proteins, the αinh is located at the C terminus and its deletion relieves autoinhibition. However, it has remained unclear how activation occurs naturally. Here, we show by structural, biophysical, and enzymatic analyses combined with in vivo data that the class III Fic protein NmFic from Neisseria meningitidis gets autoadenylylated in cis, thereby autonomously relieving autoinhibition and thus allowing subsequent adenylylation of its target, the DNA gyrase subunit GyrB. Furthermore, we show that NmFic activation is antagonized by tetramerization. The combination of autoadenylylation and tetramerization results in nonmonotonic concentration dependence of NmFic activity and a pronounced lag phase in the progress of target adenylylation. Bioinformatic analyses indicate that this elaborate dual-control mechanism is conserved throughout class III Fic proteins.


    Organizational Affiliation

    Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, CH-4056 Basel, Switzerland; christoph.dehio@unibas.ch sebastian.hiller@unibas.ch tilman.schirmer@unibas.ch.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Adenosine monophosphate-protein transferase NmFicA188Neisseria meningitidis MC58Mutation(s): 1 
Gene Names: NMB0255
EC: 2.7.7
UniProt
Find proteins for Q7DDR9 (Neisseria meningitidis serogroup B (strain MC58))
Explore Q7DDR9 
Go to UniProtKB:  Q7DDR9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7DDR9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.99 Å
  • R-Value Free: 0.125 
  • R-Value Work: 0.112 
  • R-Value Observed: 0.113 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.333α = 90
b = 50.538β = 90
c = 130.136γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 1.1: 2016-02-03
    Changes: Database references
  • Version 1.2: 2016-02-10
    Changes: Database references