5YVL | pdb_00005yvl

Crystal structure of a cyclase Hpiu5 from Fischerella sp. ATCC 43239


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 
    0.236 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5YVL

This is version 1.3 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: https://doi.org/10.1002/anie.201808231
  • Primary Citation Related Structures: 
    5YVK, 5YVL, 5YVP, 5Z53, 5Z54, 5ZFJ, 6A8X, 6A92, 6A98, 6A99, 6A9F, 6ADU

  • 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 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
    • State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, 430062, China.

Macromolecule Content 

  • Total Structure Weight: 98.78 kDa 
  • Atom Count: 6,763 
  • Modeled Residue Count: 803 
  • Deposited Residue Count: 900 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
cyclase
A, B, C, D
225Fischerella sp. ATCC 43239Mutation(s): 0 
Gene Names: hpiU5
UniProt
Find proteins for A0A076NBW8 (Fischerella sp. ATCC 43239)
Explore A0A076NBW8 
Go to UniProtKB:  A0A076NBW8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A076NBW8
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG0

Query on PG0



Download:Ideal Coordinates CCD File
G [auth B],
J [auth C],
M [auth D]
2-(2-METHOXYETHOXY)ETHANOL
C5 H12 O3
SBASXUCJHJRPEV-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
H [auth B]
I [auth B]
K [auth C]
E [auth A],
F [auth A],
H [auth B],
I [auth B],
K [auth C],
L [auth C],
N [auth D],
O [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free:  0.236 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.39α = 90
b = 114.311β = 90
c = 132.439γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2018-11-21
    Changes: Data collection, Database references
  • Version 1.2: 2018-12-26
    Changes: Data collection, Structure summary
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description