Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 44.45 kDa 
• Atom Count: 3409 
• Modelled Residue Count: 371 
• Deposited Residue Count: 405 
• Unique protein chains: 1

5Z3D

Glycosidase F290Y

• PDB DOI: 10.2210/pdb5Z3D/pdb

• Classification: HYDROLASE
• Organism(s): Kribbella flavida DSM 17836
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-01-05 Released: 2019-05-15 
• Deposition Author(s): Tanaka, Y., Chen, M., Tagami, T., Yao, M., Kimura, A.
• Funding Organization(s): Platform for Drug Discovery, Informatics, and Structural Life Science(PDIS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 0.134 
• R-Value Work: 0.113 
• R-Value Observed: 0.114 

Literature

Structural insights reveal the second base catalyst of isomaltose glucohydrolase.

Tagami, T., Chen, M., Furunaga, Y., Kikuchi, A., Sadahiro, J., Lang, W., Okuyama, M., Tanaka, Y., Iwasaki, T., Yao, M., Kimura, A.

(2022) FEBS J 289: 1118-1134

• PubMed: 34665923 
• DOI: 10.1111/febs.16237
• Primary Citation of Related Structures:  
  5Z3A, 5Z3B, 5Z3C, 5Z3D, 5Z3E, 5Z3F, 7C24, 7C25, 7C26, 7C27


• PubMed Abstract: 
  

Glycoside hydrolase family 15 (GH15) inverting enzymes contain two glutamate residues functioning as a general acid catalyst and a general base catalyst, for isomaltose glucohydrolase (IGHase), Glu178 and Glu335, respectively. Generally, a two-catalytic residue-mediated reaction exhibits a typical bell-shaped pH-activity curve. However, IGHase is found to display atypical non-bell-shaped pH-k _cat and pH-k _cat /K _m profiles, theoretically better-fitted to a three-catalytic residue-associated pH-activity curve. We determined the crystal structure of IGHase by the single-wavelength anomalous dispersion method using sulfur atoms and the cocrystal structure of a catalytic base mutant E335A with isomaltose. Although the activity of E335A was undetectable, the electron density observed in its active site pocket did not correspond to an isomaltose but a glycerol and a β-glucose, cryoprotectant, and hydrolysis product. Our structural and biochemical analyses of several mutant enzymes suggest that Tyr48 acts as a second catalytic base catalyst. Y48F mutant displayed almost equivalent specific activity to a catalytic acid mutant E178A. Tyr48, highly conserved in all GH15 members, is fixed by another Tyr residue in many GH15 enzymes; the latter Tyr is replaced by Phe290 in IGHase. The pH profile of F290Y mutant changed to a bell-shaped curve, suggesting that Phe290 is a key residue distinguishing Tyr48 of IGHase from other GH15 members. Furthermore, F290Y is found to accelerate the condensation of isomaltose from glucose by modifying a hydrogen-bonding network between Tyr290-Tyr48-Glu335. The present study indicates that the atypical Phe290 makes Tyr48 of IGHase unique among GH15 enzymes.

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Organizational Affiliation: 

Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoside hydrolase 15-related protein	A	405	Kribbella flavida DSM 17836	Mutation(s): 1  Gene Names: Kfla_1896 EC: 3.2.1.205
UniProt
Find proteins for D2PPM8 (Kribbella flavida (strain DSM 17836 / JCM 10339 / NBRC 14399)) Explore D2PPM8  Go to UniProtKB:  D2PPM8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	D [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
GOL	B [auth A], C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 0.134 
• R-Value Work: 0.113 
• R-Value Observed: 0.114 
• Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.725	α = 90
b = 104.725	β = 90
c = 89.319	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-01-05 
• Released Date: 2019-05-15 
Deposition Author(s): Tanaka, Y., Chen, M., Tagami, T., Yao, M., Kimura, A.

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Funding Organization	Location	Grant Number
Platform for Drug Discovery, Informatics, and Structural Life Science(PDIS)	Japan	--

Revision History  

• Version 1.0: 2019-05-15
  Type: Initial release
  
• Version 1.1: 2022-02-23
  Changes: Database references