7EMG

Carbonyl Reductase Variant 4 (R123C/L209P/F183Y/V61K) from Serratia marcescens complexed with NADP+

PDB DOI: https://doi.org/10.2210/pdb7EMG/pdb

Classification: OXIDOREDUCTASE
Organism(s): Serratia marcescens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2021-04-14 Released: 2021-10-06
Deposition Author(s): Zheng, Y.C., Wang, T., Bai, Y.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.259
R-Value Work: 0.200
R-Value Observed: 0.203

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Stereoselective synthesis of chiral delta-lactones via an engineered carbonyl reductase.

Wang, T., Zhang, X.Y., Zheng, Y.C., Bai, Y.P.

(2021) Chem Commun (Camb) 57: 10584-10587

PubMed: 34559867 Search on PubMed
DOI: https://doi.org/10.1039/d1cc04542c
Primary Citation of Related Structures:
7EMG

PubMed Abstract:
A carbonyl reductase variant, Sm CR _M5, from Serratia marcescens was obtained through structure-guided directed evolution. The variant showed improved specific activity (U mg ^-1) towards most of the 16 tested substrates and gave high stereoselectivities of up to 99% in the asymmetric synthesis of 13 γ-/δ-lactones. In particular, SmCR _M5 showed a 13.8-fold higher specific activity towards the model substrate, i.e. , 5-oxodecanoic acid, and gave ( R )-δ-decalactone in 99% ee with a space-time yield (STY) of 301 g L ^-1 d ^-1. The preparative synthesis of six δ-lactones in high yields and with high enantiopurities showed the feasibility of the biocatalytic synthesis of these high-value-added chemicals, providing a cost-effective and green alternative to noble-metal catalysis.

Organizational Affiliation

State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China. ybai@ecust.edu.cn.

Macromolecule Content

Total Structure Weight: 54.8 kDa
Atom Count: 3,621
Modelled Residue Count: 476
Deposited Residue Count: 504
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-oxoacyl-[acyl-carrier-protein] reductase	A, B	252	Serratia marcescens	Mutation(s): 4 Gene Names: fabG, A8A12_06940, AR325_11665, BVG93_06205, G3M86_05635, G3M87_05635, G3M88_05635, G3M89_05635, GV243_09700, HMI62_09690 EC: 1.1.1.100
UniProt
Find proteins for A0A0G8B235 (Serratia marcescens) Explore A0A0G8B235 Go to UniProtKB: A0A0G8B235
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0G8B235
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP Query on NDP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B]	C [auth A], E [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]