5VKT | pdb_00005vkt

Cinnamyl alcohol dehydrogenases (SbCAD4) from Sorghum bicolor (L.) Moench

• PDB DOI: https://doi.org/10.2210/pdb5VKT/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sorghum bicolor
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-04-22 Released: 2017-08-09 
• Deposition Author(s): Walker, A.M., Jun, S.Y., Kang, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 
  0.187 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Literature

The Enzyme Activity and Substrate Specificity of Two Major Cinnamyl Alcohol Dehydrogenases in Sorghum (Sorghum bicolor), SbCAD2 and SbCAD4.

Jun, S.Y., Walker, A.M., Kim, H., Ralph, J., Vermerris, W., Sattler, S.E., Kang, C.

(2017) Plant Physiol 174: 2128-2145

• PubMed: 28606901 
• DOI: https://doi.org/10.1104/pp.17.00576
• Primary Citation Related Structures: 
  5VKT


• PubMed Abstract: 
  

  Cinnamyl alcohol dehydrogenase (CAD) catalyzes the final step in monolignol biosynthesis, reducing sinapaldehyde, coniferaldehyde, and p -coumaraldehyde to their corresponding alcohols in an NADPH-dependent manner. Because of its terminal location in monolignol biosynthesis, the variation in substrate specificity and activity of CAD can result in significant changes in overall composition and amount of lignin. Our in-depth characterization of two major CAD isoforms, SbCAD2 (Brown midrib 6 [bmr6]) and SbCAD4, in lignifying tissues of sorghum ( Sorghum bicolor ), a strategic plant for generating renewable chemicals and fuels, indicates their similarity in both structure and activity to Arabidopsis ( Arabidopsis thaliana ) CAD5 and Populus tremuloides sinapyl alcohol dehydrogenase, respectively. This first crystal structure of a monocot CAD combined with enzyme kinetic data and a catalytic model supported by site-directed mutagenesis allows full comparison with dicot CADs and elucidates the potential signature sequence for their substrate specificity and activity. The L119W/G301F-SbCAD4 double mutant displayed its substrate preference in the order coniferaldehyde > p -coumaraldehyde > sinapaldehyde, with higher catalytic efficiency than that of both wild-type SbCAD4 and SbCAD2. As SbCAD4 is the only major CAD isoform in bmr6 mutants, replacing SbCAD4 with L119W/G301F-SbCAD4 in bmr6 plants could produce a phenotype that is more amenable to biomass processing.

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Organizational Affiliation: 
• Department of Chemistry, Washington State University, Pullman, Washington 99164.
School of Molecular Biosciences, Washington State University, Pullman, Washington 99164.
Department of Biochemistry and Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin 53726.
Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida 32610.
University of Florida, Genetics Institute, Gainesville, Florida 32610.
United States Department of Agriculture-Agricultural Research Service, Wheat, Sorghum, and Forage Research Unit, Lincoln, Nebraska 68583.
Department of Chemistry, Washington State University, Pullman, Washington 99164 [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 77.19 kDa 
• Atom Count: 6,190 
• Modeled Residue Count: 706 
• Deposited Residue Count: 724 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cinnamyl alcohol dehydrogenases (SbCAD4)	A, B	362	Sorghum bicolor	Mutation(s): 0  Gene Names: SORBI_002G195400 EC: 1.1.1.195
UniProt
Find proteins for C5XC49 (Sorghum bicolor) Explore C5XC49  Go to UniProtKB:  C5XC49

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	G [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
MLT	H [auth A]	D-MALATE C4 H6 O5 BJEPYKJPYRNKOW-UWTATZPHSA-N
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	C [auth A], D [auth A], I [auth B], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	K [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
FMT	F [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free:  0.187 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.597	α = 90
b = 74.28	β = 96.74
c = 97.288	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-09 
Deposition Author(s): Walker, A.M., Jun, S.Y., Kang, C.

Revision History  

• Version 1.0: 2017-08-09
  Type: Initial release
  
• Version 1.1: 2017-08-16
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations