6XEW

Structure of Serratia marcescens 2,3-butanediol dehydrogenase


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


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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

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

  • 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) ...

    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.


    Organizational Affiliation

    Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
2,3-butanediol dehydrogenaseA, B264Serratia marcescensMutation(s): 0 
Gene Names: budCA8A12_06140FG174_10665AB868_02667FOT62_02910G3M86_06480G3M87_06480G3M88_06480G3M89_06480SMATCC274_19470
EC: 1
UniProt
Find proteins for H9XP47 (Serratia marcescens)
Explore H9XP47 
Go to UniProtKB:  H9XP47
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
ADP
Query on ADP

Download Ideal Coordinates CCD File 
G [auth B]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
HBS
Query on HBS

Download Ideal Coordinates CCD File 
F [auth A]S,3-HYDROXYBUTAN-2-ONE
C4 H8 O2
ROWKJAVDOGWPAT-VKHMYHEASA-N
 Ligand Interaction
HBR
Query on HBR

Download Ideal Coordinates CCD File 
E [auth A]R,3-HYDROXYBUTAN-2-ONE
C4 H8 O2
ROWKJAVDOGWPAT-GSVOUGTGSA-N
 Ligand Interaction
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 = 108.171α = 90
b = 108.171β = 90
c = 82.881γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PROTEUM PLUSdata collection
PROTEUM PLUSdata scaling
MOLREPphasing

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