8XHX | pdb_00008xhx

The complex structure of PaBcmG and its natural substrate

• PDB DOI: https://doi.org/10.2210/pdb8XHX/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-12-18 Released: 2025-05-28 
• Deposition Author(s): Wu, L., Tang, G.L., Zhou, J.H.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 
  0.181 (Depositor), 0.182 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.157 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: experimental

Literature

Three distinct strategies lead to programmable aliphatic C-H oxidation in bicyclomycin biosynthesis.

Wu, L., He, J.B., Wei, W., Pan, H.X., Wang, X., Yang, S., Liang, Y., Tang, G.L., Zhou, J.

(2025) Nat Commun 16: 4651-4651

• PubMed: 40389404 
• DOI: https://doi.org/10.1038/s41467-025-58997-8
• Primary Citation Related Structures: 
  8XHP, 8XHQ, 8XHT, 8XHX, 8XHY


• PubMed Abstract: 
  

  The C-H bond functionalization has been widely used in chemical synthesis over the past decade. However, regio- and stereoselectivity still remain a significant challenge, especially for inert aliphatic C-H bonds. Here we report the mechanism of three Fe(II)/α-ketoglutarate-dependent dioxygenases in bicyclomycin synthesis, which depicts the natural tactic to sequentially hydroxylate specific C-H bonds of similar substrates (cyclodipeptides). Molecular basis by crystallographic studies, computational simulations, and site-directed mutagenesis reveals the exquisite arrangement of three enzymes using mutually orthogonal strategies to realize three different regio-selectivities. Moreover, this programmable selective hydroxylation can be extended to other cyclodipeptides. This evidence not only provides a naturally occurring showcase corresponding to the widely used methods in chemical catalysis but also expands the toolbox of biocatalysts to address the regioselective functionalization of C-H bonds.

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Organizational Affiliation: 
• Key Laboratory of Synthetic Biology, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, University of CAS, Shanghai, 200032, China.
State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of CAS, Shanghai, 200032, China.
School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China.
School of Chemistry and Material Sciences, Hangzhou Institute for Advanced Study, University of CAS, Hangzhou, 310024, China.
Henan-Macquarie University Joint Centre for Biomedical Innovation, School of Life Sciences, Henan University, Kaifeng, 475004, China.
Key Laboratory of Synthetic Biology, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, University of CAS, Shanghai, 200032, China. [e-mail].
Henan-Macquarie University Joint Centre for Biomedical Innovation, School of Life Sciences, Henan University, Kaifeng, 475004, China. [e-mail].
State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China. [e-mail].
State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of CAS, Shanghai, 200032, China. [e-mail].
School of Chemistry and Material Sciences, Hangzhou Institute for Advanced Study, University of CAS, Hangzhou, 310024, China. [e-mail].
State Key Laboratory of Microbial Technology, Nanjing Normal University, Nanjing, 210023, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 35.55 kDa 
• Atom Count: 2,789 
• Modeled Residue Count: 294 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fe/2OG dependent dioxygenase	A	306	Pseudomonas aeruginosa	Mutation(s): 0
UniProt
Find proteins for A0A241XEQ7 (Pseudomonas aeruginosa) Explore A0A241XEQ7  Go to UniProtKB:  A0A241XEQ7

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1LVG (Subject of Investigation/LOI)	C [auth A]	(3~{S},6~{S})-3-(2-methyl-2-oxidanyl-propyl)-6-[(2~{S})-4-oxidanylbutan-2-yl]piperazine-2,5-dione C12 H22 N2 O4 BJPOUTJDLWKJCE-WGTSGOJVSA-N
AKG (Subject of Investigation/LOI)	B [auth A]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
FE	D [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free:  0.181 (Depositor), 0.182 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.157 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.835	α = 90
b = 77.512	β = 90
c = 86.837	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-05-28 
Deposition Author(s): Wu, L., Tang, G.L., Zhou, J.H.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-05-28
  Type: Initial release