Crystal structure of Zhui aromatase/cyclase from Streptomcyes sp. R1128

Experimental Data Snapshot

  • Resolution: 2.39 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 

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This is version 1.2 of the entry. See complete history


Structural and Biochemical Characterization of ZhuI Aromatase/Cyclase from the R1128 Polyketide Pathway.

Ames, B.D.Lee, M.Y.Moody, C.Zhang, W.Tang, Y.Tsai, S.C.

(2011) Biochemistry 50: 8392-8406

  • DOI: https://doi.org/10.1021/bi200593m
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Aromatic polyketides comprise an important class of natural products that possess a wide range of biological activities. The cyclization of the polyketide chain is a critical control point in the biosynthesis of aromatic polyketides. The aromatase/cyclases (ARO/CYCs) are an important component of the type II polyketide synthase (PKS) and help fold the polyketide for regiospecific cyclizations of the first ring and/or aromatization, promoting two commonly observed first-ring cyclization patterns for the bacterial type II PKSs: C7-C12 and C9-C14. We had previously reported the crystal structure and enzymological analyses of the TcmN ARO/CYC, which promotes C9-C14 first-ring cyclization. However, how C7-C12 first-ring cyclization is controlled remains unresolved. In this work, we present the 2.4 Å crystal structure of ZhuI, a C7-C12-specific first-ring ARO/CYC from the type II PKS pathway responsible for the production of the R1128 polyketides. Though ZhuI possesses a helix-grip fold shared by TcmN ARO/CYC, there are substantial differences in overall structure and pocket residue composition that may be important for directing C7-C12 (rather than C9-C14) cyclization. Docking studies and site-directed mutagenesis coupled to an in vitro activity assay demonstrate that ZhuI pocket residues R66, H109, and D146 are important for enzyme function. The ZhuI crystal structure helps visualize the structure and putative dehydratase function of the didomain ARO/CYCs from KR-containing type II PKSs. The sequence-structure-function analysis described for ZhuI elucidates the molecular mechanisms that control C7-C12 first-ring polyketide cyclization and builds a foundation for future endeavors into directing cyclization patterns for engineered biosynthesis of aromatic polyketides.

  • Organizational Affiliation

    Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F
172Streptomyces sp. R1128Mutation(s): 0 
Gene Names: zhuI
Find proteins for Q9F6D3 (Streptomyces sp. R1128)
Explore Q9F6D3 
Go to UniProtKB:  Q9F6D3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9F6D3
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CXS

Download Ideal Coordinates CCD File 
H [auth A]
J [auth B]
K [auth C]
L [auth D]
M [auth D]
H [auth A],
J [auth B],
K [auth C],
L [auth D],
M [auth D],
O [auth E],
Q [auth F]
C9 H19 N O3 S
Query on K

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B],
N [auth E],
P [auth F]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.39 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.016α = 90
b = 135.731β = 90
c = 175.496γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-14
    Type: Initial release
  • Version 1.1: 2011-10-12
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations