5VKT

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.827 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1104/pp.17.00576

  • 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 ...

    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.


    Organizational Affiliation

    Department of Chemistry, Washington State University, Pullman, Washington 99164.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cinnamyl alcohol dehydrogenases (SbCAD4)
A, B
362Sorghum bicolorMutation(s): 0 
Find proteins for C5XC49 (Sorghum bicolor)
Go to UniProtKB:  C5XC49
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

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A
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
MLT
Query on MLT

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A
D-MALATE
(2R)-2-HYDROXYBUTANEDIOIC ACID; 2-HYDROXY-SUCCINIC ACID
C4 H6 O5
BJEPYKJPYRNKOW-UWTATZPHSA-N
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NAP
Query on NAP

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A
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.827 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.163 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 55.597α = 90.00
b = 74.280β = 96.74
c = 97.288γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
HKL-3000phasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-08-09
    Type: Initial release
  • Version 1.1: 2017-08-16
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Refinement description