5DP2

CurF ER cyclopropanase from curacin A biosynthetic pathway


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.96 Å
  • R-Value Free: 
    0.131 (Depositor), 0.130 (DCC) 
  • R-Value Work: 
    0.117 (Depositor), 0.120 (DCC) 
  • R-Value Observed: 
    0.117 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.4 of the entry. See complete history


Literature

Structural Basis for Cyclopropanation by a Unique Enoyl-Acyl Carrier Protein Reductase.

Khare, D.Hale, W.A.Tripathi, A.Gu, L.Sherman, D.H.Gerwick, W.H.Hakansson, K.Smith, J.L.

(2015) Structure 23: 2213-2223

  • DOI: https://doi.org/10.1016/j.str.2015.09.013
  • Primary Citation of Related Structures:  
    5DOV, 5DOZ, 5DP1, 5DP2

  • PubMed Abstract: 

    The natural product curacin A, a potent anticancer agent, contains a rare cyclopropane group. The five enzymes for cyclopropane biosynthesis are highly similar to enzymes that generate a vinyl chloride moiety in the jamaicamide natural product. The structural biology of this remarkable catalytic adaptability is probed with high-resolution crystal structures of the curacin cyclopropanase (CurF ER), an in vitro enoyl reductase (JamJ ER), and a canonical curacin enoyl reductase (CurK ER). The JamJ and CurK ERs catalyze NADPH-dependent double bond reductions typical of enoyl reductases (ERs) of the medium-chain dehydrogenase reductase (MDR) superfamily. Cyclopropane formation by CurF ER is specified by a short loop which, when transplanted to JamJ ER, confers cyclopropanase activity on the chimeric enzyme. Detection of an adduct of NADPH with the model substrate crotonyl-CoA provides indirect support for a recent proposal of a C2-ene intermediate on the reaction pathway of MDR enoyl-thioester reductases.


  • Organizational Affiliation

    Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CurF342Lyngbya majusculaMutation(s): 0 
Gene Names: curF
UniProt
Find proteins for Q6DNE7 (Lyngbya majuscula)
Explore Q6DNE7 
Go to UniProtKB:  Q6DNE7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6DNE7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download Ideal Coordinates CCD File 
B [auth A]NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.96 Å
  • R-Value Free:  0.131 (Depositor), 0.130 (DCC) 
  • R-Value Work:  0.117 (Depositor), 0.120 (DCC) 
  • R-Value Observed: 0.117 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.906α = 90
b = 47.294β = 123.44
c = 76.902γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAPClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-18
    Type: Initial release
  • Version 1.1: 2015-12-16
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.3: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Refinement description