6Z2O | pdb_00006z2o

Crystal structure of wild type OgpA from Akkermansia muciniphila in P 21 21 21


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 
    0.209 (Depositor), 0.238 (DCC) 
  • R-Value Work: 
    0.190 (Depositor) 
  • R-Value Observed: 
    0.192 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6Z2O

This is version 1.3 of the entry. See complete history

Literature

Structural basis of mammalian mucin processing by the human gut O-glycopeptidase OgpA from Akkermansia muciniphila.

Trastoy, B.Naegeli, A.Anso, I.Sjogren, J.Guerin, M.E.

(2020) Nat Commun 11: 4844-4844

  • DOI: https://doi.org/10.1038/s41467-020-18696-y
  • Primary Citation Related Structures: 
    6Z2D, 6Z2O, 6Z2P, 6Z2Q

  • PubMed Abstract: 

    Akkermansia muciniphila is a mucin-degrading bacterium commonly found in the human gut that promotes a beneficial effect on health, likely based on the regulation of mucus thickness and gut barrier integrity, but also on the modulation of the immune system. In this work, we focus in OgpA from A. muciniphila, an O-glycopeptidase that exclusively hydrolyzes the peptide bond N-terminal to serine or threonine residues substituted with an O-glycan. We determine the high-resolution X-ray crystal structures of the unliganded form of OgpA, the complex with the glycodrosocin O-glycopeptide substrate and its product, providing a comprehensive set of snapshots of the enzyme along the catalytic cycle. In combination with O-glycopeptide chemistry, enzyme kinetics, and computational methods we unveil the molecular mechanism of O-glycan recognition and specificity for OgpA. The data also contribute to understanding how A. muciniphila processes mucins in the gut, as well as analysis of post-translational O-glycosylation events in proteins.


  • Organizational Affiliation
    • Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain.

Macromolecule Content 

  • Total Structure Weight: 42.36 kDa 
  • Atom Count: 3,089 
  • Modeled Residue Count: 354 
  • Deposited Residue Count: 371 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
O-glycan protease371Akkermansia muciniphila ATCC BAA-835Mutation(s): 0 
Gene Names: Amuc_1119
UniProt
Find proteins for B2UR60 (Akkermansia muciniphila (strain ATCC BAA-835 / DSM 22959 / JCM 33894 / BCRC 81048 / CCUG 64013 / CIP 107961 / Muc))
Explore B2UR60 
Go to UniProtKB:  B2UR60
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2UR60
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



Download:Ideal Coordinates CCD File
I [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free:  0.209 (Depositor), 0.238 (DCC) 
  • R-Value Work:  0.190 (Depositor) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.379α = 90
b = 70.17β = 90
c = 94.668γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 1.1: 2021-11-03
    Changes: Data collection, Database references
  • Version 1.2: 2021-11-10
    Changes: Data collection, Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Refinement description