4PNE | pdb_00004pne

Crystal Structure of the [4+2]-Cyclase SpnF

• PDB DOI: https://doi.org/10.2210/pdb4PNE/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Saccharopolyspora spinosa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-05-23 Released: 2015-02-18 
• Deposition Author(s): Fage, C.D., Isiorho, E.A., Liu, Y.-N., Liu, H.-W., Keatinge-Clay, A.T.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Welch Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.220 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

The structure of SpnF, a standalone enzyme that catalyzes [4 + 2] cycloaddition.

Fage, C.D., Isiorho, E.A., Liu, Y., Wagner, D.T., Liu, H.W., Keatinge-Clay, A.T.

(2015) Nat Chem Biol 11: 256-258

• PubMed: 25730549 
• DOI: https://doi.org/10.1038/nchembio.1768
• Primary Citation Related Structures: 
  4PNE


• PubMed Abstract: 
  

  In the biosynthetic pathway of the spinosyn insecticides, the tailoring enzyme SpnF performs a [4 + 2] cycloaddition on a 22-membered macrolactone to forge an embedded cyclohexene ring. To learn more about this reaction, which could potentially proceed through a Diels-Alder mechanism, we determined the 1.50-Å-resolution crystal structure of SpnF bound to S-adenosylhomocysteine. This sets the stage for advanced experimental and computational studies to determine the precise mechanism of SpnF-mediated cyclization.

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Organizational Affiliation: 
• Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA.
Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas, USA.
1] Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas, USA. [2] Department of Chemistry, The University of Texas at Austin, Austin, Texas, USA.
1] Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA. [2] Department of Chemistry, The University of Texas at Austin, Austin, Texas, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 66.21 kDa 
• Atom Count: 4,434 
• Modeled Residue Count: 542 
• Deposited Residue Count: 604 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyltransferase-like protein	A, B	302	Saccharopolyspora spinosa	Mutation(s): 0  Gene Names: spnF
UniProt
Find proteins for Q9ALM7 (Saccharopolyspora spinosa) Explore Q9ALM7  Go to UniProtKB:  Q9ALM7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	C [auth A], E [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
MLI	D [auth A], F [auth B]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.220 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.74	α = 90
b = 69.35	β = 97.49
c = 83.63	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
XSCALE	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-02-18 
Deposition Author(s): Fage, C.D., Isiorho, E.A., Liu, Y.-N., Liu, H.-W., Keatinge-Clay, A.T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM106112
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM35906
Welch Foundation	United States	F-1712
Welch Foundation	United States	F-1511

Revision History  

• Version 1.0: 2015-02-18
  Type: Initial release
  
• Version 1.1: 2015-03-11
  Changes: Database references
• Version 1.2: 2015-04-01
  Changes: Database references
• Version 1.3: 2017-09-13
  Changes: Author supporting evidence, Derived calculations, Other, Source and taxonomy
• Version 1.4: 2017-11-22
  Changes: Refinement description
• Version 1.5: 2019-12-25
  Changes: Author supporting evidence
• Version 1.6: 2023-09-27
  Changes: Data collection, Database references, Refinement description