6XEW

Structure of Serratia marcescens 2,3-butanediol dehydrogenase

• PDB DOI:  https://doi.org/10.2210/pdb6XEW/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Serratia marcescens
• Expression System: Zymomonas mobilis
• Mutation(s): No 


• Deposited: 2020-06-14 Released: 2020-12-23 
• Deposition Author(s): Alahuhta, P.M., Lunin, V.V.
• Funding Organization(s): Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.214 
• R-Value Work: 0.162 

Literature

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

• PubMed: 33292448 
• 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.

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Organizational Affiliation: 

Biodiversity and Ecosystem Research, Institute of Advanced Study in Science and Technology (IASST), Guwahati, Assam, India.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 57.81 kDa 
• Atom Count: 4,303 
• Modelled Residue Count: 502 
• Deposited Residue Count: 528 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2,3-butanediol dehydrogenase	A, B	264	Serratia marcescens	Mutation(s): 0  Gene Names: budC, A8A12_06140, FG174_10665, AB868_02667, C3R40_21815, E4655_16730, FOT62_02910, HMI62_10810 EC: 1
UniProt
Find proteins for H9XP47 (Serratia marcescens) Explore H9XP47  Go to UniProtKB:  H9XP47

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	C [auth A], D [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
ADP	G [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
HBS (Subject of Investigation/LOI)	F [auth A]	S,3-HYDROXYBUTAN-2-ONE C4 H8 O2 ROWKJAVDOGWPAT-VKHMYHEASA-N
HBR (Subject of Investigation/LOI)	E [auth A]	R,3-HYDROXYBUTAN-2-ONE C4 H8 O2 ROWKJAVDOGWPAT-GSVOUGTGSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.214 
• R-Value Work: 0.162 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.171	α = 90
b = 108.171	β = 90
c = 82.881	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PROTEUM PLUS	data collection
PROTEUM PLUS	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-12-23 
Deposition Author(s): Alahuhta, P.M., Lunin, V.V.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	--

Revision History  

• Version 1.0: 2020-12-23
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description