IMPa metallopeptidase from Pseudomonas aeruginosa

Experimental Data Snapshot

  • Resolution: 1.93 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Recognition of protein-linked glycans as a determinant of peptidase activity.

Noach, I.Ficko-Blean, E.Pluvinage, B.Stuart, C.Jenkins, M.L.Brochu, D.Buenbrazo, N.Wakarchuk, W.Burke, J.E.Gilbert, M.Boraston, A.B.

(2017) Proc Natl Acad Sci U S A 114: E679-E688

  • DOI: https://doi.org/10.1073/pnas.1615141114
  • Primary Citation of Related Structures:  
    5KD2, 5KD5, 5KD8, 5KDJ, 5KDN, 5KDS, 5KDU, 5KDV, 5KDW, 5KDX

  • PubMed Abstract: 

    The vast majority of proteins are posttranslationally altered, with the addition of covalently linked sugars (glycosylation) being one of the most abundant modifications. However, despite the hydrolysis of protein peptide bonds by peptidases being a process essential to all life on Earth, the fundamental details of how peptidases accommodate posttranslational modifications, including glycosylation, has not been addressed. Through biochemical analyses and X-ray crystallographic structures we show that to hydrolyze their substrates, three structurally related metallopeptidases require the specific recognition of O-linked glycan modifications via carbohydrate-specific subsites immediately adjacent to their peptidase catalytic machinery. The three peptidases showed selectivity for different glycans, revealing protein-specific adaptations to particular glycan modifications, yet always cleaved the peptide bond immediately preceding the glycosylated residue. This insight builds upon the paradigm of how peptidases recognize substrates and provides a molecular understanding of glycoprotein degradation.

  • Organizational Affiliation

    Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Metallopeptidase891Pseudomonas aeruginosa PAO1Mutation(s): 1 
Gene Names: PA0572
Find proteins for Q9I5W4 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I5W4 
Go to UniProtKB:  Q9I5W4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I5W4
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
O4 S
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A]ZINC ION
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth A]
CA [auth A]
E [auth A]
F [auth A]
AA [auth A],
BA [auth A],
CA [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],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
C2 H6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.93 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 155.28α = 90
b = 96.41β = 124.66
c = 100.92γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-02-01
    Changes: Database references
  • Version 1.2: 2017-02-08
    Changes: Database references