6GWI

The crystal structure of Halomonas elongata amino-transferase

• PDB DOI: https://doi.org/10.2210/pdb6GWI/pdb

• Classification: TRANSFERASE
• Organism(s): Halomonas elongata DSM 2581
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-06-25 Released: 2019-05-08 
• Deposition Author(s): Gourlay, L.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.210 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 

Literature

Widely applicable background depletion step enables transaminase evolution through solid-phase screening.

Planchestainer, M., Hegarty, E., Heckmann, C.M., Gourlay, L.J., Paradisi, F.

(2019) Chem Sci 10: 5952-5958

• PubMed: 31360401 
• DOI: https://doi.org/10.1039/c8sc05712e
• Primary Citation of Related Structures:  
  6GWI


• PubMed Abstract: 
  

  Directed evolution of transaminases is a widespread technique in the development of highly sought-after biocatalysts for industrial applications. This process, however, is challenged by the limited availability of effective high-throughput protocols to evaluate mutant libraries. Here we report a rapid, reliable, and widely applicable background depletion method for solid-phase screening of transaminase variants, which was successfully applied to a transaminase from Halomonas elongata (HEWT), evolved through rounds of random mutagenesis towards a series of diverse prochiral ketones. This approach enabled the identification of transaminase variants in viable cells with significantly improved activity towards para-substituted acetophenones (up to 60-fold), as well as tetrahydrothiophen-3-one and related substrates. Rationalisation of the mutants was assisted by determination of the high-resolution wild-type HEWT crystal structure presented herein.

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Organizational Affiliation: 

University of Nottingham , School of Chemistry , University Park , Nottingham NG7 2RD , United Kingdom.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 101.66 kDa 
• Atom Count: 7,115 
• Modelled Residue Count: 899 
• Deposited Residue Count: 924 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putrescine aminotransferase	A, B	462	Halomonas elongata DSM 2581	Mutation(s): 0  Gene Names: spuC, HELO_1904 EC: 2.6.1
UniProt
Find proteins for E1V913 (Halomonas elongata (strain ATCC 33173 / DSM 2581 / NBRC 15536 / NCIMB 2198 / 1H9)) Explore E1V913  Go to UniProtKB:  E1V913

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.210 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.344	α = 83.45
b = 61.875	β = 82.58
c = 67.475	γ = 72.52

Software Package:

Software Name	Purpose
PHENIX	refinement
X-Area	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-05-08 
Deposition Author(s): Gourlay, L.J.

Revision History  

• Version 1.0: 2019-05-08
  Type: Initial release
  
• Version 1.1: 2019-08-14
  Changes: Data collection, Database references
• Version 1.2: 2020-01-15
  Changes: Data collection