9C5W | pdb_00009c5w

Crystal structure of cyclodehydratase RohQ in complex with imidazole

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.207 (Depositor), 0.207 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

Starting Model: experimental
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Literature

Structure and Mechanism of the Azomycin Biosynthetic Enzyme RohQ That Catalyzes a Spontaneous Cyclodehydration.

Wei, Z.W., Daniel-Ivad, P., Zhang, L., Ryan, K.S.

(2025) J Am Chem Soc 147: 25117-25122

  • DOI: https://doi.org/10.1021/jacs.5c04341
  • Primary Citation Related Structures: 
    9C5W, 9OQ8

  • PubMed Abstract: 

    RohQ from the azomycin biosynthetic pathway catalyzes a spontaneous cyclodehydration to form 2-aminoimidazole. Here we report the structure and mechanism of RohQ and use a serendipitously bound imidazole to pinpoint active site residues. We propose that catalysis occurs at the dimeric interface using two key aspartic acid residues for proton transfer steps to accelerate 3 × 10 4 -fold intramolecular cyclization of a guanidino group and aldehyde, releasing water. Our work expands our understanding of de novo emerged enzymes and provides the first structural and mechanistic view of a yet-unexplored protein family.

    • Organizational Affiliation: 
    • Department of Chemistry, The University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada.

Macromolecule Content 

  • Total Structure Weight: 99.14 kDa 
  • Atom Count: 6,919 
  • Modeled Residue Count: 824 
  • Deposited Residue Count: 860 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cyclodehydratase RohQA [auth E],
B [auth A],
C [auth B],
D [auth C],
E [auth D]		172Pseudomonas brassicacearumMutation(s): 0 
UniProt
Find proteins for A0A923FS92 (Pseudomonas marvdashtae)
Explore A0A923FS92 
Go to UniProtKB:  A0A923FS92
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A923FS92
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.207 (Depositor), 0.207 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.427α = 90
b = 75.427β = 90
c = 331.203γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaRGPIN-2021-02626

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-23
    Type: Initial release
  • Version 1.1: 2025-08-06
    Changes: Database references