3VMP

Crystal structure of dextranase from Streptococcus mutans in complex with 4,5-epoxypentyl alpha-D-glucopyranoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural elucidation of dextran degradation mechanism by streptococcus mutans dextranase belonging to glycoside hydrolase family 66

Suzuki, N.Kim, Y.M.Fujimoto, Z.Momma, M.Okuyama, M.Mori, H.Funane, K.Kimura, A.

(2012) J.Biol.Chem. 287: 19916-19926

  • DOI: 10.1074/jbc.M112.342444
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Dextranase is an enzyme that hydrolyzes dextran α-1,6 linkages. Streptococcus mutans dextranase belongs to glycoside hydrolase family 66, producing isomaltooligosaccharides of various sizes and consisting of at least five amino acid sequence regions. ...

    Dextranase is an enzyme that hydrolyzes dextran α-1,6 linkages. Streptococcus mutans dextranase belongs to glycoside hydrolase family 66, producing isomaltooligosaccharides of various sizes and consisting of at least five amino acid sequence regions. The crystal structure of the conserved fragment from Gln(100) to Ile(732) of S. mutans dextranase, devoid of its N- and C-terminal variable regions, was determined at 1.6 Å resolution and found to contain three structural domains. Domain N possessed an immunoglobulin-like β-sandwich fold; domain A contained the enzyme's catalytic module, comprising a (β/α)(8)-barrel; and domain C formed a β-sandwich structure containing two Greek key motifs. Two ligand complex structures were also determined, and, in the enzyme-isomaltotriose complex structure, the bound isomaltooligosaccharide with four glucose moieties was observed in the catalytic glycone cleft and considered to be the transglycosylation product of the enzyme, indicating the presence of four subsites, -4 to -1, in the catalytic cleft. The complexed structure with 4',5'-epoxypentyl-α-d-glucopyranoside, a suicide substrate of the enzyme, revealed that the epoxide ring reacted to form a covalent bond with the Asp(385) side chain. These structures collectively indicated that Asp(385) was the catalytic nucleophile and that Glu(453) was the acid/base of the double displacement mechanism, in which the enzyme showed a retaining catalytic character. This is the first structural report for the enzyme belonging to glycoside hydrolase family 66, elucidating the enzyme's catalytic machinery.


    Related Citations: 
    • Crystallization and preliminary crystallographic analysis of dextranase from Streptococcus mutans.
      Suzuki, N.,Kim, Y.M.,Fujimoto, Z.,Momma, M.,Kang, H.K.,Funane, K.,Okuyama, M.,Mori, H.,Kimura, A.
      (2011) Acta Crystallogr.,Sect.F 67: 1542


    Organizational Affiliation

    Biomolecular Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba 305-8602, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dextranase
A
643Streptococcus mutans serotype c (strain ATCC 700610 / UA159)Mutation(s): 0 
Gene Names: dexA
EC: 3.2.1.11
Find proteins for Q54443 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159))
Go to UniProtKB:  Q54443
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
E5G
Query on E5G

Download SDF File 
Download CCD File 
A
5-hydroxypentyl alpha-D-glucopyranoside
C11 H22 O7
TUXAGTBBQDBLQC-NZFPMDFQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 53.428α = 90.00
b = 89.966β = 102.25
c = 62.842γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
ADSCdata collection
REFMACrefinement
MOLREPphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-15
    Type: Initial release
  • Version 1.1: 2013-06-26
    Type: Database references