5OCM

Imine Reductase from Streptosporangium roseum in complex with NADP+ and 2,2,2-trifluoroacetophenone hydrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

New imine-reducing enzymes from beta-hydroxyacid dehydrogenases by single amino acid substitutions.

Lenz, M.Fademrecht, S.Sharma, M.Pleiss, J.Grogan, G.Nestl, B.M.

(2018) Protein Eng Des Sel 31: 109-120

  • DOI: https://doi.org/10.1093/protein/gzy006
  • Primary Citation of Related Structures:  
    5OCM

  • PubMed Abstract: 

    We report the exploration of the evolutionary relationship between imine reductases (IREDs) and other dehydrogenases. This approach is informed by the sequence similarity between these enzyme families and the recently described promiscuous activity of IREDs for the highly reactive carbonyl compound 2,2,2-trifluoroacetophenone. Using the structure of the R-selective IRED from Streptosporangium roseum (R-IRED-Sr) as a model, β-hydroxyacid dehydrogenases (βHADs) were identified as the dehydrogenases most similar to IREDs. To understand how active site differences in IREDs and βHADs enable the reduction of predominantly C = N or C = O bonds respectively, we substituted amino acid residues in βHADs with the corresponding residues from the R-IRED-Sr and were able to increase the promiscuous activity of βHADs for C = N functions by a single amino acid substitution. Variants βHADAt_K170D and βHADAt_K170F lost mainly their keto acid reduction activity and gained the ability to catalyze the reduction of imines. Moreover, the product enantiomeric purity for a bulky imine substrate could be increased from 23% ee (R-IRED-Sr) to 97% ee (βHADAt_K170D/F_F231A) outcompeting already described IRED selectivity.


  • Organizational Affiliation

    Institute of Biochemistry and Technical Biochemistry, Department of Chemistry, Universitaet Stuttgart, Allmandring 31, Stuttgart, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAD_Gly3P_dh, NAD-dependent glycerol-3-phosphate dehydrogenase
A, B, C, D, E
A, B, C, D, E, F
291Streptosporangium roseumMutation(s): 0 
Gene Names: Sros_0924
UniProt
Find proteins for D2B7Z8 (Streptosporangium roseum (strain ATCC 12428 / DSM 43021 / JCM 3005 / NI 9100))
Explore D2B7Z8 
Go to UniProtKB:  D2B7Z8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD2B7Z8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download Ideal Coordinates CCD File 
G [auth A]
J [auth B]
L [auth C]
O [auth D]
T [auth E]
G [auth A],
J [auth B],
L [auth C],
O [auth D],
T [auth E],
W [auth F]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
9RH
Query on 9RH

Download Ideal Coordinates CCD File 
H [auth A]
K [auth B]
M [auth C]
P [auth D]
U [auth E]
H [auth A],
K [auth B],
M [auth C],
P [auth D],
U [auth E],
X [auth F]
2,2,2-trifluoromethyl acetophenone hydrate
C8 H7 F3 O2
APDULARNYREANX-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
I [auth A]
N [auth C]
Q [auth D]
R [auth D]
S [auth D]
I [auth A],
N [auth C],
Q [auth D],
R [auth D],
S [auth D],
V [auth E],
Y [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.811α = 90
b = 152.434β = 90
c = 251.598γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/M006832/1

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 1.1: 2018-07-18
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description