6DWO

Crystal structure of alpha-1-2-mannosidase from Enterococcus faecalis V583


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Enterococcus faecalis alpha 1-2-mannosidase (EfMan-I): an efficient catalyst for glycoprotein N-glycan modification.

Li, Y.Li, R.Yu, H.Sheng, X.Wang, J.Fisher, A.J.Chen, X.

(2020) FEBS Lett 594: 439-451

  • DOI: https://doi.org/10.1002/1873-3468.13618
  • Primary Citation of Related Structures:  
    6DWO

  • PubMed Abstract: 

    While multiple α 1-2-mannosidases are necessary for glycoprotein N-glycan maturation in vertebrates, a single bacterial α1-2-mannosidase can be sufficient to cleave all α1-2-linked mannose residues in host glycoprotein N-glycans. We report here the characterization and crystal structure of a new α1-2-mannosidase (EfMan-I) from Enterococcus faecalis, a Gram-positive opportunistic human pathogen. EfMan-I catalyzes the cleavage of α1-2-mannose from not only oligomannoses but also high-mannose-type N-glycans on glycoproteins. Its 2.15 Å resolution crystal structure reveals a two-domain enzyme fold similar to other CAZy GH92 mannosidases. An unexpected potassium ion was observed bridging two domains near the active site. These findings support EfMan-I as an effective catalyst for in vitro N-glycan modification of glycoproteins with high-mannose-type N-glycans.


  • Organizational Affiliation

    Department of Chemistry, University of California, Davis, CA, USA.


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 V583Mutation(s): 0 
Gene Names: EF_2217
EC: 3.2.1
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
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
W [auth B],
X [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

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CA [auth C]
DA [auth C]
E [auth A]
EA [auth C]
FA [auth C]
CA [auth C],
DA [auth C],
E [auth A],
EA [auth C],
FA [auth C],
K [auth A],
L [auth A],
LA [auth D],
M [auth A],
MA [auth D],
NA [auth D],
OA [auth D],
S [auth B],
T [auth B],
U [auth B],
V [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
H [auth A]
I [auth A]
IA [auth D]
AA [auth C],
BA [auth C],
H [auth A],
I [auth A],
IA [auth D],
J [auth A],
JA [auth D],
KA [auth D],
P [auth B],
Q [auth B],
R [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA
Query on CA

Download Ideal Coordinates CCD File 
F [auth A],
GA [auth D],
N [auth B],
Y [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
G [auth A],
HA [auth D],
O [auth B],
Z [auth C]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 163.35α = 90
b = 168.99β = 90
c = 258.52γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentUnited StatesDTRA11631742

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-30
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description