4J0L

Crystal Structure of a Family GH19 Chitinase (W72A/E67Q mutant) from rye seeds in complex with two (GlcNAc)4 molecules

• PDB DOI: https://doi.org/10.2210/pdb4J0L/pdb

• Classification: HYDROLASE
• Organism(s): Secale cereale
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-01-31 Released: 2013-10-16 
• Deposition Author(s): Umemoto, N., Numata, T., Ohnuma, T., Fukamizo, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.207 
• R-Value Work: 0.182 
• R-Value Observed: 0.183 

Literature

Complete subsite mapping of a "loopful" GH19 chitinase from rye seeds based on its crystal structure

Ohnuma, T., Umemoto, N., Kondo, K., Numata, T., Fukamizo, T.

(2013) FEBS Lett 587: 2691-2697

• PubMed: 23871710 
• DOI: https://doi.org/10.1016/j.febslet.2013.07.008
• Primary Citation of Related Structures:  
  4J0L


• PubMed Abstract: 
  

  Crystallographic analysis of a mutated form of "loopful" GH19 chitinase from rye seeds a double mutant RSC-c, in which Glu67 and Trp72 are mutated to glutamine and alanine, respectively, (RSC-c-E67Q/W72A) in complex with chitin tetrasaccharide (GlcNAc)₄ revealed that the entire substrate-binding cleft was completely occupied with the sugar residues of two (GlcNAc)₄ molecules. One (GlcNAc)₄ molecule bound to subsites -4 to -1, while the other bound to subsites +1 to +4. Comparisons of the main chain conformation between liganded RSC-c-E67Q/W72A and unliganded wild type RSC-c suggested domain motion essential for catalysis. This is the first report on the complete subsite mapping of GH19 chitinase.

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Organizational Affiliation: 

Department of Advanced Bioscience, Kinki University, 3327-204 Nakamachi, Nara 631-8505, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 28.34 kDa 
• Atom Count: 2,170 
• Modelled Residue Count: 243 
• Deposited Residue Count: 244 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Basic endochitinase C	A	244	Secale cereale	Mutation(s): 2  Gene Names: rscc EC: 3.2.1.14
UniProt
Find proteins for Q9FRV0 (Secale cereale) Explore Q9FRV0  Go to UniProtKB:  Q9FRV0

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, C	4		N/A
Glycosylation Resources
GlyTouCan:  G01361SX GlyCosmos:  G01361SX GlyGen:  G01361SX

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.207 
• R-Value Work: 0.182 
• R-Value Observed: 0.183 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.783	α = 90
b = 78.783	β = 90
c = 95.123	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-16 
Deposition Author(s): Umemoto, N., Numata, T., Ohnuma, T., Fukamizo, T.

Revision History  

• Version 1.0: 2013-10-16
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary