9AUA | pdb_00009aua

PLP-dependent BesB holoenzyme

• PDB DOI: https://doi.org/10.2210/pdb9AUA/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Streptomyces achromogenes subsp. achromogenes
• Expression System: Rhodococcus jostii RHA1
• Mutation(s): No 


• Deposited: 2024-02-28 Released: 2025-07-02 
• Deposition Author(s): Hedges, J.B., Ryan, K.S.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free: 
  0.184 (Depositor), 0.177 (DCC) 
• R-Value Work: 
  0.167 (Depositor) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

Terminal alkyne formation by a pyridoxal phosphate-dependent enzyme.

Hedges, J.B., Marchand, J.A., Calvo-Tusell, C., Wei, Z.W., Millar, D.C., Garcia-Borras, M., Chang, M.C.Y., Ryan, K.S.

(2026) Nat Chem Biol 22: 77-86

• PubMed: 40562852 
• DOI: https://doi.org/10.1038/s41589-025-01954-9
• Primary Citation Related Structures: 
  9AUA, 9AUB


• PubMed Abstract: 
  

  Terminal alkyne-containing natural products can undergo the bio-orthogonal 'click' reaction of Cu(I)-catalyzed azide-alkyne cycloaddition. Recently, an enzymatic mechanism for terminal alkyne formation was discovered in the biosynthesis of L-β-ethynylserine where the pyridoxal phosphate-dependent enzyme BesB forms a rare terminal alkyne-containing amino acid, L-propargylglycine, from a vinyl halide precursor, 4-chloro-L-allylglycine. Here we present the 1.3-Å-resolution crystal structure of BesB with detailed mechanistic and computational studies. We demonstrate that BesB can reversibly catalyze the exchange of the halogen in various 4-halo-allyl-L-glycines, implying the existence of an allene intermediate, which we then also observe. Taken together, this work supports a mechanism whereby an allene is formed from deprotonation-driven halogen loss and the terminal alkyne is then formed by isomerization of the allene. Our work further expands our understanding of the catalytic repertoire of pyridoxal phosphate-dependent enzymes and will enable development of metal-free allene-forming and alkyne-forming biocatalysts.

---

Organizational Affiliation: 
• Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada.
Xilio Therapeutics, Waltham, MA, USA.
Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA.
Department of Chemical Engineering, University of Washington, Seattle, WA, USA.
Institute of Computational Chemistry and Catalysis, and Department of Chemistry, University of Girona, Girona, Spain.
Department of Molecular Biology, University of California, San Diego, La Jolla, CA, USA.
Institute of Computational Chemistry and Catalysis, and Department of Chemistry, University of Girona, Girona, Spain. [e-mail].
Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA. [e-mail].
Department of Chemistry, University of California at Berkeley, Berkeley, CA, USA. [e-mail].
Department of Chemistry, Princeton University, Princeton, NJ, USA. [e-mail].
Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 58.09 kDa 
• Atom Count: 4,280 
• Modeled Residue Count: 500 
• Deposited Residue Count: 538 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BesB	A	538	Streptomyces achromogenes subsp. achromogenes	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AN7 (Subject of Investigation/LOI)	H [auth A]	(3E)-4-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}-2-oxobut-3-enoic acid C11 H12 N O8 P FYMYHYJKCICXRI-NSCUHMNNSA-N
EDO	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	G [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG	I [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free:  0.184 (Depositor), 0.177 (DCC) 
• R-Value Work:  0.167 (Depositor) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.64	α = 90
b = 58.64	β = 90
c = 249.83	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-07-02 
Deposition Author(s): Hedges, J.B., Ryan, K.S.

---

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

Revision History  

• Version 1.0: 2025-07-02
  Type: Initial release
  
• Version 1.1: 2025-07-09
  Changes: Database references
• Version 1.2: 2026-01-07
  Changes: Database references