6OM4

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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

  • PubMed Abstract: 
  • Microcin C7 (McC) is a peptide antibiotic modified by a linkage of the terminal isoAsn amide to AMP <i>via </i> a phosphoramidate bond. Post-translational modification on this ribosomally produced heptapeptide precursor is carried out by MccB, which ...

    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.,Center for Life Sciences , Skolkov Institute of Science and Technology , 3 Nobel str. , 143026 Moscow , Russia.,Institute of Gene Biology , Russian Academy of Science , 34/5 Vavilo str. , 11934 Moscow , Russia.,Department of Biochemistry , University of Illinois at Urbana-Champaign , Illinois , USA . Email: snair@illinois.edu.,Carl Woese Institute for Genomic Biology , University of Illinois at Urbana-Champaign , Illinois , USA.,Waksman Institute for Microbiology , 190 Frelinghuysen Road , Piscataway , New Jersey , USA . Email: severik@waksman.rutgers.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MccB protein
A, B
348Escherichia coliMutation(s): 0 
Gene Names: mccB
Find proteins for Q47506 (Escherichia coli)
Go to UniProtKB:  Q47506
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Microcin C7
C, D
7N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
POP
Query on POP

Download SDF File 
Download CCD File 
A, B
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ND7
Query on ND7

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Download CCD File 
C, D
5'-O-[(S)-amino(hydroxy)phosphoryl]adenosine
C10 H15 N6 O6 P
LDEMREUBLBGZBO-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
C, D
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.155 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 55.094α = 90.00
b = 76.059β = 90.00
c = 131.902γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
PHENIXphasing
XDSdata reduction
REFMACrefinement
PHENIXmodel building
BUCCANEERmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research InstituteUnited StatesAI117210

Revision History 

  • Version 1.0: 2019-05-22
    Type: Initial release