1NKG | pdb_00001nkg

Rhamnogalacturonan lyase from Aspergillus aculeatus

• PDB DOI: https://doi.org/10.2210/pdb1NKG/pdb

• Classification: LYASE
• Organism(s): Aspergillus aculeatus
• Expression System: Aspergillus oryzae
• Mutation(s): No 


• Deposited: 2003-01-03 Released: 2004-05-25 
• Deposition Author(s): McDonough, M.A., Kadirvelraj, R., Harris, P., Poulsen, J.C., Larsen, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.186 (Depositor) 
• R-Value Work: 
  0.164 (Depositor) 
• R-Value Observed: 
  0.164 (Depositor) 

Literature

Rhamnogalacturonan lyase reveals a unique three-domain modular structure for polysaccharide lyase family 4.

McDonough, M.A., Kadirvelraj, R., Harris, P., Poulsen, J.C., Larsen, S.

(2004) FEBS Lett 565: 188-194

• PubMed: 15135077 
• DOI: https://doi.org/10.1016/j.febslet.2004.03.094
• Primary Citation of Related Structures:  
  1NKG


• PubMed Abstract: 
  

  Rhamnogalacturonan lyase (RG-lyase) specifically recognizes and cleaves alpha-1,4 glycosidic bonds between L-rhamnose and D-galacturonic acids in the backbone of rhamnogalacturonan-I, a major component of the plant cell wall polysaccharide, pectin. The three-dimensional structure of RG-lyase from Aspergillus aculeatus has been determined to 1.5 A resolution representing the first known structure from polysaccharide lyase family 4 and of an enzyme with this catalytic specificity. The 508-amino acid polypeptide displays a unique arrangement of three distinct modular domains. Each domain shows structural homology to non-catalytic domains from other carbohydrate active enzymes.

---

Organizational Affiliation: 

Centre for Crystallographic Studies, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, DK, Denmark. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PQS (software)

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: 54.67 kDa 
• Atom Count: 4,608 
• Modelled Residue Count: 508 
• Deposited Residue Count: 508 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhamnogalacturonase B	A	508	Aspergillus aculeatus	Mutation(s): 0  Gene Names: RHGB EC: 4.2.2 (PDB Primary Data), 4.2.2.23 (UniProt)
UniProt
Find proteins for Q00019 (Aspergillus aculeatus) Explore Q00019  Go to UniProtKB:  Q00019

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.186 (Depositor) 
• R-Value Work:  0.164 (Depositor) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.009	α = 90
b = 77.009	β = 90
c = 170.787	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-05-25 
Deposition Author(s): McDonough, M.A., Kadirvelraj, R., Harris, P., Poulsen, J.C., Larsen, S.

Revision History  

• Version 1.0: 2004-05-25
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2018-01-24
  Changes: Database references
• Version 1.4: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary