7FE2

Crystal structure of the mutant E494Q of GH92 alpha-1,2-mannosidase from Enterococcus faecalis ATCC 10100 in complex with alpha-1,2-mannobiose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.169 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Unlocking the Hydrolytic Mechanism of GH92 alpha-1,2-Mannosidases: Computation Inspires the use of C-Glycosides as Michaelis Complex Mimics.

Alonso-Gil, S.Parkan, K.Kaminsky, J.Pohl, R.Miyazaki, T.

(2022) Chemistry 28: e202200148-e202200148

  • DOI: https://doi.org/10.1002/chem.202200148
  • Primary Citation of Related Structures:  
    7FE1, 7FE2

  • PubMed Abstract: 

    The conformational changes in a sugar moiety along the hydrolytic pathway are key to understand the mechanism of glycoside hydrolases (GHs) and to design new inhibitors. The two predominant itineraries for mannosidases go via O S 2 →B 2,5 1 S 5 and 3 S 1 3 H 4 1 C 4 . For the CAZy family 92, the conformational itinerary was unknown. Published complexes of Bacteroides thetaiotaomicron GH92 catalyst with a S-glycoside and mannoimidazole indicate a 4 C 1 4 H 5 / 1 S 5 1 S 5 mechanism. However, as observed with the GH125 family, S-glycosides may not act always as good mimics of GH's natural substrate. Here we present a cooperative study between computations and experiments where our results predict the E 5 →B 2,5 / 1 S 5 1 S 5 pathway for GH92 enzymes. Furthermore, we demonstrate the Michaelis complex mimicry of a new kind of C-disaccharides, whose biochemical applicability was still a chimera.


  • Organizational Affiliation

    Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Dr.-Bohr-Gasse 9, 1030, Vienna, Austria.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-1,2-mannosidase
A, B, C, D
721Enterococcus faecalis ATCC 10100Mutation(s): 1 
Gene Names: WOW_02008
UniProt
Find proteins for Q832K9 (Enterococcus faecalis (strain ATCC 700802 / V583))
Explore Q832K9 
Go to UniProtKB:  Q832K9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ832K9
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-beta-D-mannopyranose
E, F, G, H
2N/A
Glycosylation Resources
GlyTouCan:  G09507TI
GlyCosmos:  G09507TI
GlyGen:  G09507TI
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
EA [auth C]
FA [auth C]
GA [auth C]
AA [auth B],
BA [auth B],
EA [auth C],
FA [auth C],
GA [auth C],
HA [auth C],
IA [auth C],
JA [auth C],
K [auth A],
L [auth A],
MA [auth D],
N [auth A],
NA [auth D],
O [auth A],
OA [auth D],
P [auth A],
PA [auth D],
Q [auth A],
QA [auth D],
R [auth A],
RA [auth D],
S [auth A],
V [auth B],
W [auth B],
X [auth B],
Z [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
M [auth A],
Y [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA
Query on CA

Download Ideal Coordinates CCD File 
CA [auth C],
I [auth A],
KA [auth D],
T [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
DA [auth C],
J [auth A],
LA [auth D],
U [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.169 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 162.626α = 90
b = 168.61β = 90
c = 260.282γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan19K15748

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-02
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references
  • Version 1.2: 2022-03-23
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Derived calculations, Refinement description