3T5M

Crystal structure of the S112A mutant of mycrocine immunity protein (MccF) with AMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.749 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and Functional Characterization of Microcin C Resistance Peptidase MccF from Bacillus anthracis.

Nocek, B.Tikhonov, A.Babnigg, G.Gu, M.Zhou, M.Makarova, K.S.Vondenhoff, G.Aerschot, A.V.Kwon, K.Anderson, W.F.Severinov, K.Joachimiak, A.

(2012) J.Mol.Biol. 420: 366-383

  • DOI: 10.1016/j.jmb.2012.04.011
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Microcin C (McC) is heptapeptide adenylate antibiotic produced by Escherichia coli strains carrying the mccABCDEF gene cluster encoding enzymes, in addition to the heptapeptide structural gene mccA, necessary for McC biosynthesis and self-immunity of ...

    Microcin C (McC) is heptapeptide adenylate antibiotic produced by Escherichia coli strains carrying the mccABCDEF gene cluster encoding enzymes, in addition to the heptapeptide structural gene mccA, necessary for McC biosynthesis and self-immunity of the producing cell. The heptapeptide facilitates McC transport into susceptible cells, where it is processed releasing a non-hydrolyzable aminoacyl adenylate that inhibits an essential aminoacyl-tRNA synthetase. The self-immunity gene mccF encodes a specialized serine peptidase that cleaves an amide bond connecting the peptidyl or aminoacyl moieties of, respectively, intact and processed McC with the nucleotidyl moiety. Most mccF orthologs from organisms other than E. coli are not linked to the McC biosynthesis gene cluster. Here, we show that a protein product of one such gene, MccF from Bacillus anthracis (BaMccF), is able to cleave intact and processed McC, and we present a series of structures of this protein. Structural analysis of apo-BaMccF and its adenosine monophosphate complex reveals specific features of MccF-like peptidases that allow them to interact with substrates containing nucleotidyl moieties. Sequence analyses and phylogenetic reconstructions suggest that several distinct subfamilies form the MccF clade of the large S66 family of bacterial serine peptidases. We show that various representatives of the MccF clade can specifically detoxify non-hydrolyzable aminoacyl adenylates differing in their aminoacyl moieties. We hypothesize that bacterial mccF genes serve as a source of bacterial antibiotic resistance.


    Organizational Affiliation

    Center for Structural Genomics of Infectious Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892-6612, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Microcin immunity protein MccF
A, B
336Bacillus anthracisMutation(s): 1 
Find proteins for A0A0F7RFM6 (Bacillus anthracis)
Go to UniProtKB:  A0A0F7RFM6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
AMP
Query on AMP

Download SDF File 
Download CCD File 
A, B
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 118.389α = 90.00
b = 118.389β = 90.00
c = 55.764γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data scaling
SBC-Collectdata collection
HKL-3000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-09-07
    Type: Initial release
  • Version 1.1: 2012-05-02
    Type: Database references
  • Version 1.2: 2012-07-25
    Type: Database references