6FYQ | pdb_00006fyq

The crystal structure of a new transaminase from the marine bacterium Virgibacillus

• PDB DOI: https://doi.org/10.2210/pdb6FYQ/pdb

• Classification: TRANSFERASE
• Organism(s): Virgibacillus pantothenticus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-03-12 Released: 2018-12-12 
• Deposition Author(s): Gourlay, L.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.219 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Strategic single point mutation yields a solvent- and salt-stable transaminase from Virgibacillus sp. in soluble form.

Guidi, B., Planchestainer, M., Contente, M.L., Laurenzi, T., Eberini, I., Gourlay, L.J., Romano, D., Paradisi, F., Molinari, F.

(2018) Sci Rep 8: 16441-16441

• PubMed: 30401905 
• DOI: https://doi.org/10.1038/s41598-018-34434-3
• Primary Citation Related Structures: 
  6FYQ


• PubMed Abstract: 
  

  A new transaminase (VbTA) was identified from the genome of the halotolerant marine bacterium Virgibacillus 21D. Following heterologous expression in Escherichia coli, it was located entirely in the insoluble fraction. After a single mutation, identified via sequence homology analyses, the VbTA T16F mutant was successfully expressed in soluble form and characterised. VbTA T16F showed high stability towards polar organic solvents and salt exposure, accepting mainly hydrophobic aromatic amine and carbonyl substrates. The 2.0 Å resolution crystal structure of VbTA T16F is here reported, and together with computational calculations, revealed that this mutation is crucial for correct dimerisation and thus correct folding, leading to soluble protein expression.

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Organizational Affiliation: 
• Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy.
School of Chemistry, University of Nottingham, University Park, Nottingham, NG& 2RD, UK.
Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, Milan, Italy.
Department of Biosciences, University of Milan, Milan, Italy.
School of Chemistry, University of Nottingham, University Park, Nottingham, NG& 2RD, UK. [e-mail].
Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy. [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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 53.71 kDa 
• Atom Count: 3,520 
• Modeled Residue Count: 443 
• Deposited Residue Count: 484 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
amine transaminase	A	484	Virgibacillus pantothenticus	Mutation(s): 0  EC: 2.6.1.18
UniProt
Find proteins for A0A4P1LYG1 (Virgibacillus pantothenticus) Explore A0A4P1LYG1  Go to UniProtKB:  A0A4P1LYG1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP (Subject of Investigation/LOI)	B [auth A]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
EDO	C [auth A], D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.219 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.886	α = 90
b = 100.886	β = 90
c = 97.411	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
SCALA	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-12-12 
Deposition Author(s): Gourlay, L.J.

Revision History  

• Version 1.0: 2018-12-12
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Advisory, Data collection, Database references, Refinement description