6OM4

The structure of Microcin C7 biosynthetic enzyme MccB in complex with N-formylated MccA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 

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Literature

Biosynthesis of the RiPP trojan horse nucleotide antibiotic microcin C is directed by theN-formyl of the peptide precursor.

Dong, S.H.Kulikovsky, A.Zukher, I.Estrada, P.Dubiley, S.Severinov, K.Nair, S.K.

(2019) Chem Sci 10: 2391-2395

  • DOI: 10.1039/c8sc03173h
  • Primary Citation of Related Structures:  
    6OM4

  • PubMed Abstract: 
  • Microcin C7 (McC) is a peptide antibiotic modified by a linkage of the terminal isoAsn amide to AMP via a phosphoramidate bond. Post-translational modification on this ribosomally produced heptapeptide precursor is carried out by MccB, which consumes two equivalents of ATP to generate the N-P linkage ...

    Microcin C7 (McC) is a peptide antibiotic modified by a linkage of the terminal isoAsn amide to AMP via a phosphoramidate bond. Post-translational modification on this ribosomally produced heptapeptide precursor is carried out by MccB, which consumes two equivalents of ATP to generate the N-P linkage. We demonstrate that MccB only efficiently processes the precursor heptapeptide that retains the N -formylated initiator Met (fMet). Binding studies and kinetic measurements evidence the role of the N -formyl moiety. Structural data show that the N -formyl peptide binding results in an ordering of residues in the MccB "crossover loop", which dictates specificity in homologous ubiquitin activating enzymes. The N -formyl peptide exhibits substrate inhibition, and cannot be displaced from MccB by the desformyl counterpart. Such substrate inhibition may be a strategy to avert unwanted McC buildup and avert toxicity in the cytoplasm of producing organisms.


    Organizational Affiliation

    Center for Biophysics and Quantitative Biology , University of Illinois at Urbana-Champaign , Illinois , USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MccB proteinA, B348Escherichia coliMutation(s): 0 
Gene Names: mccB
UniProt
Find proteins for Q47506 (Escherichia coli)
Explore Q47506 
Go to UniProtKB:  Q47506
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Microcin C7C, D7Escherichia coliMutation(s): 0 
Gene Names: mccA
UniProt
Find proteins for Q47505 (Escherichia coli)
Explore Q47505 
Go to UniProtKB:  Q47505
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
C, DL-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.094α = 90
b = 76.059β = 90
c = 131.902γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata scaling
PHENIXmodel building
BUCCANEERmodel building
PHENIXphasing
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesAI117210

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-22
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Author supporting evidence