5TZ6

Crystal Structure of CurJ Dehydratase H978F Inactive Mutant In Complex with Compound 21


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Vinylogous Dehydration by a Polyketide Dehydratase Domain in Curacin Biosynthesis.

Fiers, W.D.Dodge, G.J.Sherman, D.H.Smith, J.L.Aldrich, C.C.

(2016) J Am Chem Soc 138: 16024-16036

  • DOI: https://doi.org/10.1021/jacs.6b09748
  • Primary Citation of Related Structures:  
    5TZ5, 5TZ6, 5TZ7

  • PubMed Abstract: 

    Polyketide synthase (PKS) enzymes continue to hold great promise as synthetic biology platforms for the production of novel therapeutic agents, biofuels, and commodity chemicals. Dehydratase (DH) catalytic domains play an important role during polyketide biosynthesis through the dehydration of the nascent polyketide intermediate to provide olefins. Our understanding of the detailed mechanistic and structural underpinning of DH domains that control substrate specificity and selectivity remains limited, thus hindering our efforts to rationally re-engineer PKSs. The curacin pathway houses a rare plurality of possible double bond permutations containing conjugated olefins as well as both cis- and trans-olefins, providing an unrivaled model system for polyketide dehydration. All four DH domains implicated in curacin biosynthesis were characterized in vitro using synthetic substrates, and activity was measured by LC-MS/MS analysis. These studies resulted in complete kinetic characterization of the all-trans-trienoate-forming CurK-DH, whose k cat of 72 s -1 is more than 3 orders of magnitude greater than that of any previously reported PKS DH domain. A novel stereospecific mechanism for diene formation involving a vinylogous enolate intermediate is proposed for the CurJ and CurH DHs on the basis of incubation studies with truncated substrates. A synthetic substrate was co-crystallized with a catalytically inactive Phe substitution in the His-Asp catalytic dyad of CurJ-DH to elucidate substrate-enzyme interactions. The resulting complex suggested the structural basis for dienoate formation and provided the first glimpse into the enzyme-substrate interactions essential for the formation of olefins in polyketide natural products. This examination of both canonical and non-canonical dehydration mechanisms reveals hidden catalytic activity inherent in some DH domains that may be leveraged for future applications in synthetic biology.


  • Organizational Affiliation

    Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota , Minneapolis, Minnesota 55455, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CurJ
A, B
308Moorena producens 3LMutation(s): 1 
Gene Names: LYNGBM3L_74460
UniProt
Find proteins for F4Y426 (Moorena producens 3L)
Explore F4Y426 
Go to UniProtKB:  F4Y426
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF4Y426
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7OD
Query on 7OD

Download Ideal Coordinates CCD File 
C [auth A](2E,5R)-5-hydroxy-2-methylhept-2-enoic acid
C8 H14 O3
FUDLYCKELQYCSU-PTYLAXBQSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.55α = 90
b = 70.584β = 90
c = 176.018γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Refinement description