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 7ZGM | pdb_00007zgm

Plant N-glycan specific alpha-1,3-mannosidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 
    0.172 (Depositor), 0.166 (DCC) 
  • R-Value Work: 
    0.133 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7ZGM

This is version 1.3 of the entry. See complete history. 

Literature

Plant N -glycan breakdown by human gut Bacteroides.

Crouch, L.I., Urbanowicz, P.A., Basle, A., Cai, Z.P., Liu, L., Voglmeir, J., Melo Diaz, J.M., Benedict, S.T., Spencer, D.I.R., Bolam, D.N.

(2022) Proc Natl Acad Sci U S A 119: e2208168119-e2208168119

  • DOI: https://doi.org/10.1073/pnas.2208168119
  • Primary Citation Related Structures: 
    7ZGM, 7ZGN

  • PubMed Abstract: 

    The major nutrients available to the human colonic microbiota are complex glycans derived from the diet. To degrade this highly variable mix of sugar structures, gut microbes have acquired a huge array of different carbohydrate-active enzymes (CAZymes), predominantly glycoside hydrolases, many of which have specificities that can be exploited for a range of different applications. Plant N -glycans are prevalent on proteins produced by plants and thus components of the diet, but the breakdown of these complex molecules by the gut microbiota has not been explored. Plant N -glycans are also well characterized allergens in pollen and some plant-based foods, and when plants are used in heterologous protein production for medical applications, the N -glycans present can pose a risk to therapeutic function and stability. Here we use a novel genome association approach for enzyme discovery to identify a breakdown pathway for plant complex N -glycans encoded by a gut Bacteroides species and biochemically characterize five CAZymes involved, including structures of the PNGase and GH92 α-mannosidase. These enzymes provide a toolbox for the modification of plant N -glycans for a range of potential applications. Furthermore, the keystone PNGase also has activity against insect-type N -glycans, which we discuss from the perspective of insects as a nutrient source.


  • Organizational Affiliation: 
    • Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 80.64 kDa 
  • Atom Count: 6,324 
  • Modeled Residue Count: 702 
  • Deposited Residue Count: 709 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycoside hydrolase family 92 protein709Phocaeicola massiliensis B84634 = Timone 84634 = DSM 17679 = JCM 13223Mutation(s): 0 
Gene Names: HMPREF1534_02484
UniProt
Find proteins for U6RD63 (Phocaeicola massiliensis B84634 = Timone 84634 = DSM 17679 = JCM 13223)
Explore U6RD63 
Go to UniProtKB:  U6RD63
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupU6RD63
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA

Query on CA



Download:Ideal Coordinates CCD File
R [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
K

Query on K



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
D [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free:  0.172 (Depositor), 0.166 (DCC) 
  • R-Value Work:  0.133 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.941α = 90
b = 84.335β = 90
c = 132.581γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Cootmodel building
MolProbitymodel building
PHASERphasing
pointlessdata scaling
xia2data reduction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/M029018/1

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-07
    Type: Initial release
  • Version 1.1: 2022-09-28
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary