5Y2A | pdb_00005y2a

Crystal structure of Ostrinia furnacalis Group II chitinase catalytic domain 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.186 (Depositor), 0.187 (DCC) 
  • R-Value Work: 
    0.167 (Depositor), 0.168 (DCC) 

Starting Model: experimental
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This is version 2.2 of the entry. See complete history

Literature

Structural analysis of group II chitinase (ChtII) catalysis completes the puzzle of chitin hydrolysis in insects

Chen, W.Qu, M.Zhou, Y.Yang, Q.

(2018) J Biological Chem 293: 2652-2660

  • DOI: https://doi.org/10.1074/jbc.RA117.000119
  • Primary Citation Related Structures: 
    5Y29, 5Y2A, 5Y2B, 5Y2C

  • PubMed Abstract: 

    Chitin is a linear homopolymer of N -acetyl-β-d-glucosamines and a major structural component of insect cuticles. Chitin hydrolysis involves glycoside hydrolase family 18 (GH18) chitinases. In insects, chitin hydrolysis is essential for periodic shedding of the old cuticle ecdysis and proceeds via a pathway different from that in the well studied bacterial chitinolytic system. Group II chitinase (ChtII) is a widespread chitinolytic enzyme in insects and contains the greatest number of catalytic domains and chitin-binding domains among chitinases. In Lepidopterans, ChtII and two other chitinases, ChtI and Chi-h, are essential for chitin hydrolysis. Although ChtI and Chi-h have been well studied, the role of ChtII remains elusive. Here, we investigated the structure and enzymology of Of ChtII, a ChtII derived from the insect pest Ostrinia furnacalis We present the crystal structures of two catalytically active domains of Of ChtII, Of ChtII-C1 and Of ChtII-C2, both in unliganded form and complexed with chitooligosaccharide substrates. We found that Of ChtII-C1 and Of ChtII-C2 both possess long, deep substrate-binding clefts with endochitinase activities. Of ChtII exhibited structural characteristics within the substrate-binding cleft similar to those in Of Chi-h and Of ChtI. However, Of ChtII lacked structural elements favoring substrate binding beyond the active sites, including an extra wall structure present in Of Chi-h. Nevertheless, the numerous domains in Of ChtII may compensate for this difference; a truncation containing one catalytic domain and three chitin-binding modules ( Of ChtII-B4C1) displayed activity toward insoluble polymeric substrates that was higher than those of Of Chi-h and Of ChtI. Our observations provide the last piece of the puzzle of chitin hydrolysis in insects.


  • Organizational Affiliation
    • State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, Dalian 116024, China.

Macromolecule Content 

  • Total Structure Weight: 89.09 kDa 
  • Atom Count: 6,998 
  • Modeled Residue Count: 766 
  • Deposited Residue Count: 766 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
insect group II chitinase
A, B
383Ostrinia furnacalisMutation(s): 0 
EC: 3.2.1.14
UniProt
Find proteins for A0A221ZS22 (Ostrinia furnacalis)
Explore A0A221ZS22 
Go to UniProtKB:  A0A221ZS22
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A221ZS22
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D
6N-Glycosylation
Glycosylation Resources
GlyTouCan: G60005GQ
GlyCosmos: G60005GQ
GlyGen: G60005GQ

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.186 (Depositor), 0.187 (DCC) 
  • R-Value Work:  0.167 (Depositor), 0.168 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.637α = 90
b = 90.654β = 116.41
c = 74.856γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
Cootmodel building
PHENIXphasing
HKL-3000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Database references
  • Version 1.2: 2018-03-07
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 2.2: 2024-11-20
    Changes: Structure summary