2WYI

Structure of the Streptococcus pyogenes family GH38 alpha-mannosidase complexed with swainsonine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure and Kinetic Investigation of Streptococcus Pyogenes Family Gh38 Alpha-Mannosidase

Suits, M.D.L.Zhu, Y.Taylor, E.J.Zechel, D.L.Gilbert, H.J.Davies, G.J.

(2010) Plos One 5: E9006

  • DOI: 10.1371/journal.pone.0009006
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The enzymatic hydrolysis of alpha-mannosides is catalyzed by glycoside hydrolases (GH), termed alpha-mannosidases. These enzymes are found in different GH sequence-based families. Considerable research has probed the role of higher eukaryotic "GH38" ...

    The enzymatic hydrolysis of alpha-mannosides is catalyzed by glycoside hydrolases (GH), termed alpha-mannosidases. These enzymes are found in different GH sequence-based families. Considerable research has probed the role of higher eukaryotic "GH38" alpha-mannosides that play a key role in the modification and diversification of hybrid N-glycans; processes with strong cellular links to cancer and autoimmune disease. The most extensively studied of these enzymes is the Drosophila GH38 alpha-mannosidase II, which has been shown to be a retaining alpha-mannosidase that targets both alpha-1,3 and alpha-1,6 mannosyl linkages, an activity that enables the enzyme to process GlcNAc(Man)(5)(GlcNAc)(2) hybrid N-glycans to GlcNAc(Man)(3)(GlcNAc)(2). Far less well understood is the observation that many bacterial species, predominantly but not exclusively pathogens and symbionts, also possess putative GH38 alpha-mannosidases whose activity and specificity is unknown.


    Organizational Affiliation

    York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALPHA-MANNOSIDASE
A, B
923Streptococcus pyogenes serotype M1Mutation(s): 0 
Find proteins for Q99YP5 (Streptococcus pyogenes serotype M1)
Go to UniProtKB:  Q99YP5
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
PG0
Query on PG0

Download SDF File 
Download CCD File 
A, B
2-(2-METHOXYETHOXY)ETHANOL
PEG 6000
C5 H12 O3
SBASXUCJHJRPEV-UHFFFAOYSA-N
 Ligand Interaction
SWA
Query on SWA

Download SDF File 
Download CCD File 
A, B
1S-8AB-OCTAHYDRO-INDOLIZIDINE-1A,2A,8B-TRIOL
SWAINSONINE
C8 H15 N O3
FXUAIOOAOAVCGD-WCTZXXKLSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SWAKi: 18000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.187 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 178.680α = 90.00
b = 178.680β = 90.00
c = 198.237γ = 90.00
Software Package:
Software NamePurpose
RESOLVEphasing
SHARPphasing
SHELXphasing
REFMACrefinement
PHASERmodel building
PHASERphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-02-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance