7TCL

Crystal structure of P.IsnB complexed with tyrosine isonitrile

• PDB DOI: https://doi.org/10.2210/pdb7TCL/pdb

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


• Deposited: 2021-12-26 Released: 2022-08-31 
• Deposition Author(s): Kim, W., Zhang, Y.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 0.212 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Literature

Elucidation of divergent desaturation pathways in the formation of vinyl isonitrile and isocyanoacrylate.

Kim, W., Chen, T.Y., Cha, L., Zhou, G., Xing, K., Canty, N.K., Zhang, Y., Chang, W.C.

(2022) Nat Commun 13: 5343-5343

• PubMed: 36097268 
• DOI: https://doi.org/10.1038/s41467-022-32870-4
• Primary Citation of Related Structures:  
  7TCL


• PubMed Abstract: 
  

  Two different types of desaturations are employed by iron- and 2-oxoglutarate-dependent (Fe/2OG) enzymes to construct vinyl isonitrile and isocyanoacrylate moieties found in isonitrile-containing natural products. A substrate-bound protein structure reveals a plausible strategy to affect desaturation and hints at substrate promiscuity of these enzymes. Analogs are synthesized and used as mechanistic probes to validate structural observations. Instead of proceeding through hydroxylated intermediate as previously proposed, a plausible carbocation species is utilized to trigger C=C bond installation. These Fe/2OG enzymes can also accommodate analogs with opposite chirality and different functional groups including isonitrile-(D)-tyrosine, N-formyl tyrosine, and phloretic acid, while maintaining the reaction selectivity.

---

Organizational Affiliation: 

McKetta Department of Chemical Engineering, University of Texas, Austin, TX, USA.

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: 33.57 kDa 
• Atom Count: 2,297 
• Modelled Residue Count: 259 
• Deposited Residue Count: 281 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TauD/TfdA family dioxygenase	A [auth X]	281	Photorhabdus	Mutation(s): 0  Gene Names: GPY51_01460
UniProt
Find proteins for Q7N3A2 (Photorhabdus laumondii subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01)) Explore Q7N3A2  Go to UniProtKB:  Q7N3A2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
I3J (Subject of Investigation/LOI)	F [auth X]	(2S)-3-(4-hydroxyphenyl)-2-isocyanopropanoic acid C10 H9 N O3 YAVJAMZLLTZAJX-VIFPVBQESA-N
SO4	C [auth X], D [auth X], E [auth X]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MN	B [auth X]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 0.212 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.868	α = 90
b = 58.375	β = 90
c = 102.589	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-08-31 
Deposition Author(s): Kim, W., Zhang, Y.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM104896
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM125882

Revision History  

• Version 1.0: 2022-08-31
  Type: Initial release
  
• Version 1.1: 2022-09-28
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description