6KLG

Crystal Structure of the Zea Mays laccase 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

wwPDB Validation 3D Report Full Report



Literature

Structural basis for monolignol oxidation by a maize laccase.

Xie, T.Liu, Z.Wang, G.

(2020) Nat Plants 6: 231-237

  • DOI: 10.1038/s41477-020-0595-5
  • Primary Citation of Related Structures:  
    6KLG, 6KLJ, 6KLI

  • PubMed Abstract: 
  • Plant laccases catalyse the oxidation of monolignols in lignification, a process reinforcing the cell wall of many different cell types that provide mechanical support, nutrient transportation and defence against pathogens in plants 1 . Th ...

    Plant laccases catalyse the oxidation of monolignols in lignification, a process reinforcing the cell wall of many different cell types that provide mechanical support, nutrient transportation and defence against pathogens in plants 1 . The isozymes display a broad range of substrate preferences. Here, the substrate preference of a laccase (ZmLac3) from Zea mays (maize) was characterized. The crystal structure of ZmLac3 revealed a compact and deep substrate-binding pocket, and the binding modes of sinapyl alcohol (SinA) and coniferyl alcohol (ConA) were solved. On the basis of structural data and kinetics analysis, we propose that the regionalization of polar and hydrophobic surfaces in the binding pocket of ZmLac3 is vital for defining the orientation of SinA/ConA binding. The extra methoxyl group in SinA makes substantial contributions to interactions between SinA and ZmLac3, which are absent in the ZmLac3-ConA complex. In summary, the polar and hydrophobic interactions between SinA/ConA and ZmLac3 determine the binding positions of the monolignols in ZmLac3. These results provide valuable insight about ZmLac3 catalysis and should aid industrial processes that use plant laccases.


    Organizational Affiliation

    The Innovative Academy of Seed Design (INASEED), Chinese Academy of Sciences, Beijing, China. wanggg@cib.ac.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LaccaseA550Zea maysMutation(s): 0 
Gene Names: lac3
EC: 1.10.3.2
Find proteins for Q2PAJ1 (Zea mays)
Explore Q2PAJ1 
Go to UniProtKB:  Q2PAJ1
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B, C
2 N-Glycosylation
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CU
Query on CU

Download CCD File 
A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
OXY
Query on OXY

Download CCD File 
A
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.977α = 90
b = 111.977β = 90
c = 208.094γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-01-01
    Type: Initial release
  • Version 1.1: 2020-03-11
    Changes: Data collection, Database references
  • Version 1.2: 2020-04-01
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary