5DU9

First condensation domain of the calcium-dependent antibiotic synthetase in complex with substrate analogue 2a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Chemical Probes Allow Structural Insight into the Condensation Reaction of Nonribosomal Peptide Synthetases.

Bloudoff, K.Alonzo, D.A.Schmeing, T.M.

(2016) Cell Chem Biol 23: 331-339

  • DOI: 10.1016/j.chembiol.2016.02.012
  • Primary Citation of Related Structures:  
    5DUA, 5DU9

  • PubMed Abstract: 
  • Nonribosomal peptide synthetases (NRPSs) synthesize a vast variety of small molecules, including antibiotics, antitumors, and immunosuppressants. The NRPS condensation (C) domain catalyzes amide bond formation, the central chemical step in nonribosomal peptide synthesis ...

    Nonribosomal peptide synthetases (NRPSs) synthesize a vast variety of small molecules, including antibiotics, antitumors, and immunosuppressants. The NRPS condensation (C) domain catalyzes amide bond formation, the central chemical step in nonribosomal peptide synthesis. The catalytic mechanism and substrate determinants of the reaction are under debate. We developed chemical probes to structurally study the NRPS condensation reaction. These substrate analogs become covalently tethered to a cysteine introduced near the active site, to mimic covalent substrate delivery by carrier domains. They are competent substrates in the condensation reaction and behave similarly to native substrates. Co-crystal structures show C domain-substrate interactions, and suggest that the catalytic histidine's principle role is to position the α-amino group for nucleophilic attack. Structural insight provided by these co-complexes also allowed us to alter the substrate specificity profile of the reaction with a single point mutation.


    Organizational Affiliation

    Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Francesco Bellini Life Sciences Building, Room 465, Montréal, QC H3G 0B1, Canada. Electronic address: martin.schmeing@mcgill.ca.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CDA peptide synthetase IA, B450Streptomyces coelicolor A3(2)Mutation(s): 1 
Gene Names: SCO3230
UniProt
Find proteins for Q9Z4X6 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Explore Q9Z4X6 
Go to UniProtKB:  Q9Z4X6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UM2
Query on UM2

Download Ideal Coordinates CCD File 
E [auth A], G [auth B](2S)-2-amino-N-butyl-propanamide
C7 H16 N2 O
XXYQJGUBGFEJMV-LURJTMIESA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 213.428α = 90
b = 213.428β = 90
c = 52.901γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada106615

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-30
    Type: Initial release
  • Version 1.1: 2020-01-08
    Changes: Author supporting evidence, Database references, Derived calculations