4LGX

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
R-Value Work: 0.162
R-Value Observed: 0.163

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/srep15657
Primary Citation of 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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A8GFD6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A]	C [auth A], D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OMT Query on 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
R-Value Work: 0.162
R-Value Observed: 0.163
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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-10-02

Deposition Author(s):

Revision History (Full details and data files)

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