7N4W | pdb_00007n4w

Complex structure of ROTU4 with rotundine

• PDB DOI: https://doi.org/10.2210/pdb7N4W/pdb

• Classification: TRANSCRIPTION
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-06-04 Released: 2022-06-29 
• Deposition Author(s): Kim, W., Zhang, Y.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 
  0.173 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.151 (Depositor) 
• R-Value Observed: 
  0.152 (Depositor) 

Starting Model: experimental

Literature

Using fungible biosensors to evolve improved alkaloid biosyntheses.

d'Oelsnitz, S., Kim, W., Burkholder, N.T., Javanmardi, K., Thyer, R., Zhang, Y., Alper, H.S., Ellington, A.D.

(2022) Nat Chem Biol 18: 981-989

• PubMed: 35799063 
• DOI: https://doi.org/10.1038/s41589-022-01072-w
• Primary Citation Related Structures: 
  7N4W, 7N4Z, 7N53, 7N54


• PubMed Abstract: 
  

  A key bottleneck in the microbial production of therapeutic plant metabolites is identifying enzymes that can improve yield. The facile identification of genetically encoded biosensors can overcome this limitation and become part of a general method for engineering scaled production. We have developed a combined screening and selection approach that quickly refines the affinities and specificities of generalist transcription factors; using RamR as a starting point, we evolve highly specific (>100-fold preference) and sensitive (half-maximum effective concentration (EC ₅₀ ) < 30 μM) biosensors for the alkaloids tetrahydropapaverine, papaverine, glaucine, rotundine and noscapine. High-resolution structures reveal multiple evolutionary avenues for the malleable effector-binding site and the creation of new pockets for different chemical moieties. These sensors further enabled the evolution of a streamlined pathway for tetrahydropapaverine, a precursor to four modern pharmaceuticals, collapsing multiple methylation steps into a single evolved enzyme. Our methods for evolving biosensors enable the rapid engineering of pathways for therapeutic alkaloids.

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Organizational Affiliation: 
• Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA. [e-mail].
McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA.
Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.
Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA.
Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA. [e-mail].

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)

Macromolecule Content 

• Total Structure Weight: 22.69 kDa 
• Atom Count: 1,607 
• Modeled Residue Count: 183 
• Deposited Residue Count: 194 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ROTU4	A	194	Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S	Mutation(s): 0
UniProt
Find proteins for A0A0F6AY66 (Salmonella typhimurium (strain 14028s / SGSC 2262)) Explore A0A0F6AY66  Go to UniProtKB:  A0A0F6AY66

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P4V (Subject of Investigation/LOI)	D [auth A]	rotundine C21 H25 N O4 AEQDJSLRWYMAQI-QGZVFWFLSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free:  0.173 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.151 (Depositor) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.88	α = 90
b = 50.61	β = 90.12
c = 46.079	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-06-29 
Deposition Author(s): Kim, W., Zhang, Y.

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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: 2022-06-29
  Type: Initial release
  
• Version 1.1: 2022-07-20
  Changes: Database references
• Version 1.2: 2022-09-07
  Changes: Database references
• Version 1.3: 2023-10-18
  Changes: Data collection, Refinement description