8OF7 | pdb_00008of7

Cyc15 Diels Alderase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 
    0.215 (Depositor), 0.205 (DCC) 
  • R-Value Work: 
    0.187 (Depositor) 
  • R-Value Observed: 
    0.189 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 8OF7

This is version 1.2 of the entry. See complete history

Literature

Interrogation of an Enzyme Library Reveals the Catalytic Plasticity of Naturally Evolved [4+2] Cyclases.

Zorn, K.Back, C.R.Barringer, R.Chadimova, V.Manzo-Ruiz, M.Mbatha, S.Z.Mobarec, J.C.Williams, S.E.van der Kamp, M.W.Race, P.R.Willis, C.L.Hayes, M.A.

(2023) Chembiochem 24: e202300382-e202300382

  • DOI: https://doi.org/10.1002/cbic.202300382
  • Primary Citation Related Structures: 
    8OF7

  • PubMed Abstract: 

    Stereoselective carbon-carbon bond forming reactions are quintessential transformations in organic synthesis. One example is the Diels-Alder reaction, a [4+2] cycloaddition between a conjugated diene and a dienophile to form cyclohexenes. The development of biocatalysts for this reaction is paramount for unlocking sustainable routes to a plethora of important molecules. To obtain a comprehensive understanding of naturally evolved [4+2] cyclases, and to identify hitherto uncharacterised biocatalysts for this reaction, we constructed a library comprising forty-five enzymes with reported or predicted [4+2] cycloaddition activity. Thirty-one library members were successfully produced in recombinant form. In vitro assays employing a synthetic substrate incorporating a diene and a dienophile revealed broad-ranging cycloaddition activity amongst these polypeptides. The hypothetical protein Cyc15 was found to catalyse an intramolecular cycloaddition to generate a novel spirotetronate. The crystal structure of this enzyme, along with docking studies, establishes the basis for stereoselectivity in Cyc15, as compared to other spirotetronate cyclases.


  • Organizational Affiliation
    • Compound Synthesis and Management, Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 431 83, Mölndal, Sweden.

Macromolecule Content 

  • Total Structure Weight: 35.68 kDa 
  • Atom Count: 2,200 
  • Modeled Residue Count: 258 
  • Deposited Residue Count: 306 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Rhs family protein
A, B
153Streptomyces sp. NL15-2KMutation(s): 0 
Gene Names: SNL152K_10620

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG

Query on PEG



Download:Ideal Coordinates CCD File
D [auth A],
H [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SER

Query on SER



Download:Ideal Coordinates CCD File
L [auth A]SERINE
C3 H7 N O3
MTCFGRXMJLQNBG-REOHCLBHSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
P [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
GLY

Query on GLY



Download:Ideal Coordinates CCD File
F [auth A],
I [auth A],
K [auth A],
R [auth B],
W [auth B]
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
IMD

Query on IMD



Download:Ideal Coordinates CCD File
C [auth A],
G [auth A]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
EDO

Query on EDO



Download:Ideal Coordinates CCD File
E [auth A]
J [auth A]
M [auth A]
N [auth A]
O [auth A]
E [auth A],
J [auth A],
M [auth A],
N [auth A],
O [auth A],
Q [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free:  0.215 (Depositor), 0.205 (DCC) 
  • R-Value Work:  0.187 (Depositor) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.14α = 90
b = 65.14β = 90
c = 180.14γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data scaling
MOLREPphasing
xia2data reduction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/T001968/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/T008741/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/L01386X/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/M012107/1

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-21
    Type: Initial release
  • Version 1.1: 2023-07-26
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Data collection