5WUL

Serratia marcescens short-chain dehydrogenase/reductase F98A/F202L


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure-guided design of Serratia marcescens short-chain dehydrogenase/reductase for stereoselective synthesis of (R)-phenylephrine.

Liu, J.-S.Kuan, Y.-C.Tsou, Y.Lin, T.-Y.Hsu, W.-H.Yang, M.-T.Lin, J.-Y.Wang, W.-C.

(2018) Sci Rep 8: 2316-2316

  • DOI: https://doi.org/10.1038/s41598-018-19235-y
  • Primary Citation of Related Structures:  
    5WUL, 5WUW, 5WVA

  • PubMed Abstract: 

    Bioconversion is useful to produce optically pure enantiomers in the pharmaceutical industry, thereby avoiding problems with side reactions during organic synthesis processes. A short-chain dehydrogenase/reductase from Serratia marcescens BCRC 10948 (SmSDR) can stereoselectively convert 1-(3-hydroxyphenyl)-2-(methylamino) ethanone (HPMAE) into (R)-phenylephrine [(R)-PE], which is marketed medically as a nasal decongestant agent. The whole-cell conversion process for the synthesis of (R)-PE using SmSDR was reported to have an unexpectedly low conversion rate. We reported the crystal structure of the SmSDR and designed profitable variants to improve the enzymatic activity by structure-guided approach. Several important residues in the structure were observed to form hydrophobic clusters that stabilize the mobile loops surrounding the pocket. Of these, Phe98 and Phe202 face toward each other and connect the upper curvature from the two arms (i.e., the α7 helix and loopβ4-α4). The mutant structure of the double substitutions (F98YF202Y) exhibited a hydrogen bond between the curvatures that stabilizes the flexible arms. Site-directed mutagenesis characterization revealed that the mutations (F98Y, F98YF202Y, and F98YF202L) of the flexible loops that stabilize the region exhibited a higher transformation activity toward HPMAE. Together, our results suggest a robust structure-guided approach that can be used to generate a valuable engineered variant for pharmaceutical applications.


  • Organizational Affiliation

    Institute of Molecular and Cellular Biology & Department of Life Science, National Tsing Hua University, Hsinchu, 300, Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Short-chain dehydrogenase
A, B
287Serratia marcescensMutation(s): 2 
UniProt
Find proteins for A0A192ICX3 (Serratia marcescens)
Explore A0A192ICX3 
Go to UniProtKB:  A0A192ICX3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A192ICX3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.799α = 90
b = 83.799β = 90
c = 114.253γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description