8OF7 | pdb_00008of7

Cyc15 Diels Alderase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 
    0.215 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

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


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 of 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rhs family protein
A, B
153Streptomyces sp. NL15-2KMutation(s): 0 
Gene Names: SNL152K_10620
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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), 0.200 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.200 (DCC) 
  • 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