5DP2 | pdb_00005dp2

CurF ER cyclopropanase from curacin A biosynthetic pathway

• PDB DOI: https://doi.org/10.2210/pdb5DP2/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Lyngbya majuscula
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-09-12 Released: 2015-11-18 
• Deposition Author(s): Khare, D., Smith, J.L.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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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), 0.116 (DCC) 
• R-Value Observed: 
  0.117 (Depositor) 

Starting Model: experimental

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

• PubMed: 26526850 
• DOI: https://doi.org/10.1016/j.str.2015.09.013
• Primary Citation 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.

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Organizational Affiliation: 
• Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109, USA.
Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA.
Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109, USA; Department Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109-1065, USA.
Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109, USA; Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA; Department Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109-1065, USA; Department Microbiology & Immunology, University of Michigan, Ann Arbor, MI 48109-5620, USA.
Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA 92093, USA.
Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109, USA; Department Biological Chemistry, University of Michigan, Ann Arbor, MI 48109-0600, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 38.96 kDa 
• Atom Count: 3,444 
• Modeled Residue Count: 335 
• Deposited Residue Count: 342 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CurF	A	342	Lyngbya majuscula	Mutation(s): 0  Gene Names: curF
UniProt
Find proteins for Q6DNE7 (Lyngbya majuscula) Explore Q6DNE7  Go to UniProtKB:  Q6DNE7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	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), 0.116 (DCC) 
• R-Value Observed: 0.117 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.906	α = 90
b = 47.294	β = 123.44
c = 76.902	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-11-18 
Deposition Author(s): Khare, D., Smith, J.L.

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

Revision History  

• 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