6HTO | pdb_00006hto

Tryptophan lyase 'empty state'

• PDB DOI: https://doi.org/10.2210/pdb6HTO/pdb

• Classification: ANTIBIOTIC
• Organism(s): Streptomyces actuosus
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2018-10-04 Released: 2018-11-21 
• Deposition Author(s): Amara, P., Mouesca, J.M., Bella, M., Martin, L., Saragaglia, C., Gambarelli, S., Nicolet, Y.
• Funding Organization(s): French National Research Agency, French Infrastructure for Integrated Structural Biology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.192 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

Radical S-Adenosyl-l-methionine Tryptophan Lyase (NosL): How the Protein Controls the Carboxyl Radical •CO2-Migration.

Amara, P., Mouesca, J.M., Bella, M., Martin, L., Saragaglia, C., Gambarelli, S., Nicolet, Y.

(2018) J Am Chem Soc 140: 16661-16668

• PubMed: 30418774 
• DOI: https://doi.org/10.1021/jacs.8b09142
• Primary Citation Related Structures: 
  6HTK, 6HTM, 6HTO


• PubMed Abstract: 
  

  The radical S-adenosyl-l-methionine tryptophan lyase uses radical-based chemistry to convert l-tryptophan into 3-methyl-2-indolic acid, a fragment in the biosynthesis of the thiopeptide antibiotic nosiheptide. This complex reaction involves several successive steps corresponding to (i) the activation by a specific hydrogen-atom abstraction, (ii) an unprecedented •CO ₂ ^- radical migration, (iii) a cyanide fragment release, and (iv) the termination of the radical-based reaction. In vitro study of this reaction is made more difficult because the enzyme produces a significant amount of a shunt product instead of the natural product. Here, using a combination of X-ray crystallography, electron paramagnetic resonance spectroscopy, and quantum and hybrid quantum mechanical/molecular mechanical calculations, we have deciphered the fine mechanism of the key •CO ₂ ^- radical migration, highlighting how the preorganized active site of the protein tightly controls this reaction.

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Organizational Affiliation: 
• Univ. Grenoble Alpes, CEA, CNRS, IBS , Metalloproteins Unit , F-38000 Grenoble , France.
Univ. Grenoble Alpes, CNRS, CEA , INAC-SyMMES , 38000 Grenoble , France.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 91.49 kDa 
• Atom Count: 7,311 
• Modeled Residue Count: 759 
• Deposited Residue Count: 800 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-methyl-2-indolic acid synthase	A, B	400	Streptomyces actuosus	Mutation(s): 0  Gene Names: nosL, nocL, DMT42_23170
UniProt
Find proteins for C6FX51 (Streptomyces actuosus) Explore C6FX51  Go to UniProtKB:  C6FX51

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4	C [auth A], O [auth B]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
5AD	E [auth A], Q [auth B]	5'-DEOXYADENOSINE C10 H13 N5 O3 XGYIMTFOTBMPFP-KQYNXXCUSA-N
MET	D [auth A], P [auth B]	METHIONINE C5 H11 N O2 S FFEARJCKVFRZRR-BYPYZUCNSA-N
GOL	F [auth A], R [auth B], S [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], T [auth B], U [auth B], V [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.192 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.97	α = 90
b = 92.61	β = 98.73
c = 94.46	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-11-21 
Deposition Author(s): Amara, P., Mouesca, J.M., Bella, M., Martin, L., Saragaglia, C., Gambarelli, S., Nicolet, Y.

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Funding Organization	Location	Grant Number
French National Research Agency	France	ANR-16-CE29-0019
French Infrastructure for Integrated Structural Biology	France	ANR-10-INSB-05-02
French Infrastructure for Integrated Structural Biology	France	ANR-10-LABX-49-01

Revision History  

• Version 1.0: 2018-11-21
  Type: Initial release
  
• Version 1.1: 2018-11-28
  Changes: Data collection, Database references
• Version 1.2: 2019-04-24
  Changes: Data collection, Database references
• Version 1.3: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description