8FRG

Mouse acidic mammalian chitinase, catalytic domain in complex with N,N'-diacetylchitobiose at pH 5.43

  • Classification: HYDROLASE
  • Organism(s): Mus musculus
  • Expression System: Cricetulus griseus
  • Mutation(s): No 

  • Deposited: 2023-01-06 Released: 2023-03-15 
  • Deposition Author(s): Diaz, R.E., Fraser, J.S.
  • Funding Organization(s): Other government, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase.

Diaz, R.E.Ecker, A.K.Correy, G.J.Asthana, P.Young, I.D.Faust, B.Thompson, M.C.Seiple, I.B.Van Dyken, S.J.Locksley, R.M.Fraser, J.S.

(2024) bioRxiv 

  • DOI: https://doi.org/10.1101/2023.06.03.542675
  • Primary Citation of Related Structures:  
    8FG5, 8FG7, 8FR9, 8FRA, 8FRB, 8FRC, 8FRD, 8FRG, 8GCA

  • PubMed Abstract: 

    Chitin is an abundant biopolymer and pathogen-associated molecular pattern that stimulates a host innate immune response. Mammals express chitin-binding and chitin-degrading proteins to remove chitin from the body. One of these proteins, Acidic Mammalian Chitinase (AMCase), is an enzyme known for its ability to function under acidic conditions in the stomach but is also active in tissues with more neutral pHs, such as the lung. Here, we used a combination of biochemical, structural, and computational modeling approaches to examine how the mouse homolog (mAMCase) can act in both acidic and neutral environments. We measured kinetic properties of mAMCase activity across a broad pH range, quantifying its unusual dual activity optima at pH 2 and 7. We also solved high resolution crystal structures of mAMCase in complex with oligomeric GlcNAcn, the building block of chitin, where we identified extensive conformational ligand heterogeneity. Leveraging these data, we conducted molecular dynamics simulations that suggest how a key catalytic residue could be protonated via distinct mechanisms in each of the two environmental pH ranges. These results integrate structural, biochemical, and computational approaches to deliver a more complete understanding of the catalytic mechanism governing mAMCase activity at different pH. Engineering proteins with tunable pH optima may provide new opportunities to develop improved enzyme variants, including AMCase, for therapeutic purposes in chitin degradation.


  • Organizational Affiliation

    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acidic mammalian chitinase
A, B
397Mus musculusMutation(s): 0 
Gene Names: ChiaChia1
EC: 3.2.1.14
UniProt
Find proteins for Q91XA9 (Mus musculus)
Explore Q91XA9 
Go to UniProtKB:  Q91XA9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ91XA9
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, E, F
2N/AN/A
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose
D
2N/AN/A
Glycosylation Resources
GlyTouCan:  G05026ZL
GlyCosmos:  G05026ZL
GlyGen:  G05026ZL
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.893α = 90
b = 105.041β = 90
c = 70.812γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
DIALSdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentT29IP0554
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP30GM124169

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-15
    Type: Initial release
  • Version 1.1: 2023-06-14
    Changes: Database references
  • Version 1.2: 2023-07-19
    Changes: Database references
  • Version 1.3: 2024-04-10
    Changes: Data collection, Database references