Structure of Serratia marcescens 2,3-butanediol dehydrogenase mutant Q247A

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.168 

Starting Model: experimental
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Phylogenetics-based identification and characterization of a superior 2,3-butanediol dehydrogenase for Zymomonas mobilis expression.

Subramanian, V.Lunin, V.V.Farmer, S.J.Alahuhta, M.Moore, K.T.Ho, A.Chaudhari, Y.B.Zhang, M.Himmel, M.E.Decker, S.R.

(2020) Biotechnol Biofuels 13: 186-186

  • DOI: https://doi.org/10.1186/s13068-020-01820-x
  • Primary Citation of Related Structures:  
    6VSP, 6XEW, 6XEX

  • PubMed Abstract: 

    Zymomonas mobilis has recently been shown to be capable of producing the valuable platform biochemical, 2,3-butanediol (2,3-BDO). Despite this capability, the production of high titers of 2,3-BDO is restricted by several physiological parameters. One such bottleneck involves the conversion of acetoin to 2,3-BDO, a step catalyzed by 2,3-butanediol dehydrogenase (Bdh). Several Bdh enzymes have been successfully expressed in Z. mobilis, although a highly active enzyme is yet to be identified for expression in this host. Here, we report the application of a phylogenetic approach to identify and characterize a superior Bdh, followed by validation of its structural attributes using a mutagenesis approach. Of the 11 distinct bdh genes that were expressed in Z. mobilis, crude extracts expressing Serratia marcescens Bdh (SmBdh) were found to have the highest activity (8.89 µmol/min/mg), when compared to other Bdh enzymes (0.34-2.87 µmol/min/mg). The SmBdh crystal structure was determined through crystallization with cofactor (NAD + ) and substrate (acetoin) molecules bound in the active site. Active SmBdh was shown to be a tetramer with the active site populated by a Gln247 residue contributed by the diagonally opposite subunit. SmBdh showed a more extensive supporting hydrogen-bond network in comparison to the other well-studied Bdh enzymes, which enables improved substrate positioning and substrate specificity. This protein also contains a short α6 helix, which provides more efficient entry and exit of molecules from the active site, thereby contributing to enhanced substrate turnover. Extending the α6 helix to mimic the lower activity Enterobacter cloacae (EcBdh) enzyme resulted in reduction of SmBdh function to nearly 3% of the total activity. In great contrast, reduction of the corresponding α6 helix of the EcBdh to mimic the SmBdh structure resulted in ~ 70% increase in its activity. This study has demonstrated that SmBdh is superior to other Bdhs for expression in Z. mobilis for 2,3-BDO production. SmBdh possesses unique structural features that confer biochemical advantage to this protein. While coordinated active site formation is a unique structural characteristic of this tetrameric complex, the smaller α6 helix and extended hydrogen network contribute towards improved activity and substrate promiscuity of the enzyme.

  • Organizational Affiliation

    Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA. venkat.subramanian@nrel.gov.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2,3-butanediol dehydrogenase
A, B
264Serratia marcescensMutation(s): 1 
Gene Names: budCA8A12_06140FG174_10665
EC: 1.1.1
Find proteins for H9XP47 (Serratia marcescens)
Explore H9XP47 
Go to UniProtKB:  H9XP47
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH9XP47
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD (Subject of Investigation/LOI)
Query on NAD

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
C21 H27 N7 O14 P2
Query on ADP

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C10 H15 N5 O10 P2
Query on GOL

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C3 H8 O3
Query on EDO

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F [auth A]
G [auth A]
H [auth A]
I [auth A]
L [auth B]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
L [auth B],
M [auth B],
N [auth B]
C2 H6 O2
Query on NA

Download Ideal Coordinates CCD File 
J [auth A],
O [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.168 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.675α = 90
b = 108.675β = 90
c = 82.948γ = 90
Software Package:
Software NamePurpose
PROTEUM PLUSdata reduction
PROTEUM PLUSdata collection

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-23
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description