6ADU

Crystal structure of an enzyme in complex with ligand C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The Crystal Structure of a Class of Cyclases that Catalyze the Cope Rearrangement.

Chen, C.C.Hu, X.Tang, X.Yang, Y.Ko, T.P.Gao, J.Zheng, Y.Huang, J.W.Yu, Z.Li, L.Han, S.Cai, N.Zhang, Y.Liu, W.Guo, R.T.

(2018) Angew Chem Int Ed Engl 57: 15060-15064

  • DOI: 10.1002/anie.201808231
  • Primary Citation of Related Structures:  
    5Z53, 5Z54, 5YVK, 5YVL, 5YVP, 5ZFJ, 6ADU, 6A9F, 6A8X, 6A99

  • PubMed Abstract: 
  • Found recently in stignomatales, the Stig cyclases catalyze the Cope rearrangement and intramolecular cyclization to produce complex indole alkaloids. Five crystal structures were solved of subfamily 1 and 2 Stig cyclases, which adopt a β-sandwich fo ...

    Found recently in stignomatales, the Stig cyclases catalyze the Cope rearrangement and intramolecular cyclization to produce complex indole alkaloids. Five crystal structures were solved of subfamily 1 and 2 Stig cyclases, which adopt a β-sandwich fold like the non-catalytic carbohydrate-binding motif. Several complex structures were also determined of indole-based compounds, which are bound to the hydrophobic terminal cavity, where a conserved Asp residue makes an H-bond to the indole N and triggers the acid-catalyzed Cope rearrangement. Through analyzing the enzyme-ligand interactions and mutagenesis experiments, several aromatic residues were found important in catalysis. Apart from a common substrate binding mode and catalytic mechanism, potential subfamily variations that may attribute to the different product specificity are implicated. These results shall expand our scope of enzymology, in particular for further investigation of the biosynthetic Cope rearrangement.


    Organizational Affiliation

    Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
acyclaseA, B, C, D227Fischerella ambigua UTEX 1903Mutation(s): 0 
Find proteins for V5TER4 (Fischerella ambigua UTEX 1903)
Explore V5TER4 
Go to UniProtKB:  V5TER4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9UL
Query on 9UL

Download CCD File 
A, B, C, D
(3~{Z})-3-(1-methylpyrrolidin-2-ylidene)indole
C13 H14 N2
HNNADWWHLOZSTI-ACCUITESSA-N
 Ligand Interaction
TRS
Query on TRS

Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
CA
Query on CA

Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.773α = 90
b = 256.546β = 90
c = 36.043γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-08-21
    Type: Initial release
  • Version 1.1: 2020-03-04
    Changes: Database references