1IDK

PECTIN LYASE A

• PDB DOI: https://doi.org/10.2210/pdb1IDK/pdb

• Classification: LYASE
• Organism(s): Aspergillus niger
• Mutation(s): No 


• Deposited: 1996-10-04 Released: 1997-10-15 
• Deposition Author(s): Mayans, O., Scott, M., Connerton, I., Gravesen, T., Benen, J., Visser, J., Pickersgill, R., Jenkins, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.232 
• R-Value Work: 0.188 
• R-Value Observed: 0.188 

Literature

Two crystal structures of pectin lyase A from Aspergillus reveal a pH driven conformational change and striking divergence in the substrate-binding clefts of pectin and pectate lyases.

Mayans, O., Scott, M., Connerton, I., Gravesen, T., Benen, J., Visser, J., Pickersgill, R., Jenkins, J.

(1997) Structure 5: 677-689

• PubMed: 9195887 
• DOI: https://doi.org/10.1016/s0969-2126(97)00222-0
• Primary Citation of Related Structures:  
  1IDJ, 1IDK


• PubMed Abstract: 
  

  Microbial pectin and pectate lyases are virulence factors that degrade the pectic components of the plant cell wall. The homogalacturan backbone of pectin varies in its degree of methylation from the highly methylated and relatively hydrophobic form known as pectin, to the fully demethylated and highly charged form known as pectate. Methylated and demethylated regions of pectin are cleaved by pectin lyase and calcium-dependent pectate lyases, respectively. Protein engineering of lyases specific for particular patterns of methylation, will yield modified pectins of high value to the food and pharmaceutical industries.

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Organizational Affiliation: 

Department of Food Macromolecular Science, Institute of Food Research, Earley Gate, Whiteknights Road, Reading, RG6 6BZ, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37.98 kDa 
• Atom Count: 2,850 
• Modelled Residue Count: 359 
• Deposited Residue Count: 359 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PECTIN LYASE A	A	359	Aspergillus niger	Mutation(s): 0  EC: 4.2.2.10
UniProt
Find proteins for Q01172 (Aspergillus niger) Explore Q01172  Go to UniProtKB:  Q01172

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.232 
• R-Value Work: 0.188 
• R-Value Observed: 0.188 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.4	α = 90
b = 83.5	β = 90
c = 93.4	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
ROTAVATA	data reduction
Agrovata	data reduction
X-PLOR	model building
X-PLOR	refinement
CCP4	data scaling
ROTAVATA	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-10-15 
Deposition Author(s): Mayans, O., Scott, M., Connerton, I., Gravesen, T., Benen, J., Visser, J., Pickersgill, R., Jenkins, J.

Revision History  

• Version 1.0: 1997-10-15
  Type: Initial release
  
• Version 1.1: 2008-03-05
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-04-03
  Changes: Data collection, Database references, Refinement description