9OQ8 | pdb_00009oq8

Crystal structure of selenomethionine-substituted cyclodehydratase RohQ

PDB DOI: https://doi.org/10.2210/pdb9OQ8/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Pseudomonas brassicacearum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-05-20 Released: 2025-07-23
Deposition Author(s): Wei, Z.-W., Daniel-Ivad, P., Ryan, K.S.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free:
0.265 (Depositor), 0.272 (DCC)
R-Value Work:
0.222 (Depositor), 0.230 (DCC)
R-Value Observed:
0.224 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 9OQ8

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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

PubMed: 40644315 Search on PubMed
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: 112.34 kDa
Atom Count: 6,361
Modeled Residue Count: 809
Deposited Residue Count: 960
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RohQ	A, B, C [auth E], D [auth C], E [auth D]	192	Pseudomonas brassicacearum	Mutation(s): 0
UniProt
Find proteins for A0A923FS92 (Pseudomonas marvdashtae) Explore A0A923FS92 Go to UniProtKB: A0A923FS92
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A923FS92
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IMD (Subject of Investigation/LOI) Query on IMD Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth B] SDF format, chain F [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth B] MOL2 format, chain F [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth B] mmCIF format, chain F [auth A]	F [auth A], G [auth B], H [auth D]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C [auth E], D [auth C], E [auth D]	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free: 0.265 (Depositor), 0.272 (DCC)
R-Value Work: 0.222 (Depositor), 0.230 (DCC)
R-Value Observed: 0.224 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.299	α = 90
b = 75.299	β = 90
c = 333.701	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
Coot	model building
AutoSol	phasing
DIALS	data scaling
Blu-Ice	data collection

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-23

Deposition Author(s):

Daniel-Ivad, P.

Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	RGPIN-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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.