4XB3 | pdb_00004xb3

Structure of dextran glucosidase

• PDB DOI: https://doi.org/10.2210/pdb4XB3/pdb

• Classification: HYDROLASE
• Organism(s): Streptococcus mutans UA159
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-12-16 Released: 2015-08-26 
• Deposition Author(s): Kobayashi, M., Kato, K., Yao, M.
• Funding Organization(s): the Japan Society for the Promotion of Science, the Ministry of Education, Culture, Sports, Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 
  0.219 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Literature

Structural insights into the catalytic reaction that is involved in the reorientation of Trp238 at the substrate-binding site in GH13 dextran glucosidase

Kobayashi, M., Saburi, W., Nakatsuka, D., Hondoh, H., Kato, K., Okuyama, M., Mori, H., Kimura, A., Yao, M.

(2015) FEBS Lett 589: 484-489

• PubMed: 25595454 
• DOI: https://doi.org/10.1016/j.febslet.2015.01.005
• Primary Citation Related Structures: 
  4WLC, 4XB3


• PubMed Abstract: 
  

  Streptococcus mutans dextran glucosidase (SmDG) belongs to glycoside hydrolase family 13, and catalyzes both the hydrolysis of substrates such as isomaltooligosaccharides and subsequent transglucosylation to form α-(1→6)-glucosidic linkage at the substrate non-reducing ends. Here, we report the 2.4Å resolution crystal structure of glucosyl-enzyme intermediate of SmDG. In the obtained structure, the Trp238 side-chain that constitutes the substrate-binding site turned away from the active pocket, concurrently with conformational changes of the nucleophile and the acid/base residues. Different conformations of Trp238 in each reaction stage indicated its flexibility. Considering the results of kinetic analyses, such flexibility may reflect a requirement for the reaction mechanism of SmDG.

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Organizational Affiliation: 
• Graduate School of Life Science, Hokkaido University, Kita-10, Nishi-8, Kita-ku, Sapporo 060-0810, Japan.
Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kita-ku, Sapporo 060-8589, Japan.
Graduate School of Life Science, Hokkaido University, Kita-10, Nishi-8, Kita-ku, Sapporo 060-0810, Japan; Faculty of Advanced Life Science, Hokkaido University, Kita-10, Nishi-8, Kita-ku, Sapporo 060-0810, Japan.

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: 62.51 kDa 
• Atom Count: 4,749 
• Modeled Residue Count: 536 
• Deposited Residue Count: 536 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucan 1,6-alpha-glucosidase	A	536	Streptococcus mutans UA159	Mutation(s): 2  Gene Names: dexB, SMU_883 EC: 3.2.1.70
UniProt
Find proteins for Q99040 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159)) Explore Q99040  Go to UniProtKB:  Q99040

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P6G	F [auth A]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
CA	B [auth A], C [auth A], D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.219 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.151	α = 90
b = 82.55	β = 90
c = 103.559	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-08-26 
Deposition Author(s): Kobayashi, M., Kato, K., Yao, M.

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Funding Organization	Location	Grant Number
the Japan Society for the Promotion of Science	Japan	24-871
the Ministry of Education, Culture, Sports, Science and Technology	Japan	--

Revision History  

• Version 1.0: 2015-08-26
  Type: Initial release
  
• Version 1.1: 2020-02-05
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations