Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 22.35 kDa 
• Atom Count: 2041 
• Modelled Residue Count: 181 
• Deposited Residue Count: 188 
• Unique protein chains: 1

5CKL

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

• PDB DOI: 10.2210/pdb5CKL/pdb

• Classification: TRANSFERASE
• Organism(s): Neisseria meningitidis MC58
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-07-15 Released: 2016-01-27 
• Deposition Author(s): Stanger, F.V., Schirmer, T.

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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 

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

• PubMed: 26787847 
• 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. 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.

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Organizational Affiliation: 

Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, CH-4056 Basel, Switzerland; [e-mail] [e-mail] [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosine monophosphate-protein transferase NmFic	A	188	Neisseria meningitidis MC58	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	C [auth A], D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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 = 35.333	α = 90
b = 50.538	β = 90
c = 130.136	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-07-15 
• Released Date: 2016-01-27 
Deposition Author(s): Stanger, F.V., Schirmer, T.

Revision History  

• 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