5FF5

Crystal Structure of SeMet PaaA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.93 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Post-translational Claisen Condensation and Decarboxylation en Route to the Bicyclic Core of Pantocin A.

Ghodge, S.V.Biernat, K.A.Bassett, S.J.Redinbo, M.R.Bowers, A.A.

(2016) J Am Chem Soc 138: 5487-5490

  • DOI: https://doi.org/10.1021/jacs.5b13529
  • Primary Citation of Related Structures:  
    5FF5

  • PubMed Abstract: 

    Pantocin A (PA) is a member of the growing family of ribosomally encoded and post-translationally modified peptide natural products (RiPPs). PA is much smaller than most known RiPPs, a tripeptide with a tight bicyclic core that appears to be cleaved from the middle of a larger 30-residue precursor peptide. We show here that the enzyme PaaA catalyzes the double dehydration and decarboxylation of two glutamic acid residues in the 30-residue precursor PaaP. Further truncates of PaaP leader and follower peptide sequences demonstrate the different impacts of these two regions on PaaA-mediated tailoring and delineate an essential role for the follower sequence in the decarboxylation step. The crystal structure of apo PaaA is reported, allowing identification of structural features that set PaaA apart from other homologous enzymes that typically do not catalyze such extended post-translational chemistry. Together, these data reveal how additional chemistry can be extracted from a ubiquitous enzyme family toward ribosomally derived peptide natural product biosynthesis and suggest that more examples of such enzymes likely exist in untapped genomic space.


  • Organizational Affiliation

    Division of Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill , Eshelmann School of Pharmacy, Chapel Hill, North Carolina 27599, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PaaA
A, B
381Pantoea agglomeransMutation(s): 0 
Gene Names: paaA
UniProt
Find proteins for Q9ZAR3 (Enterobacter agglomerans)
Explore Q9ZAR3 
Go to UniProtKB:  Q9ZAR3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ZAR3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.93 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.218 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.962α = 90
b = 170.409β = 90
c = 64.323γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
AutoSolphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-27
    Type: Initial release
  • Version 1.1: 2016-05-18
    Changes: Database references