4LGX | pdb_00004lgx

Structure of Chitinase D from Serratia proteamaculans revealed an unusually constrained substrate binding site

• PDB DOI: https://doi.org/10.2210/pdb4LGX/pdb

• Classification: HYDROLASE
• Organism(s): Serratia proteamaculans 568
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-06-30 Released: 2013-10-02 
• Deposition Author(s): Madhuprakash, J., Singh, A., Kumar, S., Sinha, M., Kaur, P., Sharma, S., Podile, A.R., Singh, T.P.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free: 
  0.176 (Depositor), 0.174 (DCC) 
• R-Value Work: 
  0.162 (Depositor) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

Inverse relationship between chitobiase and transglycosylation activities of chitinase-D from Serratia proteamaculans revealed by mutational and biophysical analyses.

Madhuprakash, J., Bobbili, K.B., Moerschbacher, B.M., Singh, T.P., Swamy, M.J., Podile, A.R.

(2015) Sci Rep 5: 15657-15657

• PubMed: 26493546 
• DOI: https://doi.org/10.1038/srep15657
• Primary Citation Related Structures: 
  4LGX


• PubMed Abstract: 
  

  Serratia proteamaculans chitinase-D (SpChiD) has a unique combination of hydrolytic and transglycosylation (TG) activities. The TG activity of SpChiD can be used for large-scale production of chito-oligosaccharides (CHOS). The multiple activities (hydrolytic and/or chitobiase activities and TG) of SpChiD appear to be strongly influenced by the substrate-binding cleft. Here, we report the unique property of SpChiD substrate-binding cleft, wherein, the residues Tyr28, Val35 and Thr36 control chitobiase activity and the residues Trp160 and Trp290 are crucial for TG activity. Mutants with reduced (V35G and T36G/F) or no (SpChiDΔ30-42 and Y28A) chitobiase activity produced higher amounts of the quantifiable even-chain TG product with degree of polymerization (DP)-6, indicating that the chitobiase and TG activities are inversely related. In addition to its unprecedented catalytic properties, unlike other chitinases, the single modular SpChiD showed dual unfolding transitions. Ligand-induced thermal stability studies with the catalytically inactive mutant of SpChiD (E153A) showed that the transition temperature increased upon binding of CHOS with DP2-6. Isothermal titration calorimetry experiments revealed the exceptionally high binding affinities for E153A to CHOS with DP2-6. These observations strongly support that the architecture of SpChiD substrate-binding cleft adopted to control chitobiase and TG activities, in addition to usual chitinase-mediated hydrolysis.

---

Organizational Affiliation: 
• Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, India.
School of Chemistry, University of Hyderabad, Gachibowli, Hyderabad, India.
Institute for Biology and Biotechnology of Plants, WWU, Münster University, Münster, Germany.
Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 45.02 kDa 
• Atom Count: 3,773 
• Modeled Residue Count: 398 
• Deposited Residue Count: 406 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoside hydrolase family 18	A	406	Serratia proteamaculans 568	Mutation(s): 0  Gene Names: Spro_2725 EC: 3.2.1.14
UniProt
Find proteins for A8GFD6 (Serratia proteamaculans (strain 568)) Explore A8GFD6  Go to UniProtKB:  A8GFD6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	B [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OMT	A	L-PEPTIDE LINKING	C5 H11 N O4 S		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free:  0.176 (Depositor), 0.174 (DCC) 
• R-Value Work:  0.162 (Depositor) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.33	α = 90
b = 87.156	β = 90
c = 59.546	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-02 
Deposition Author(s): Madhuprakash, J., Singh, A., Kumar, S., Sinha, M., Kaur, P., Sharma, S., Podile, A.R., Singh, T.P.

Revision History  

• Version 1.0: 2013-10-02
  Type: Initial release
  
• Version 1.1: 2016-07-27
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary