5KDV

IMPa metallopeptidase from Pseudomonas aeruginosa

• PDB DOI:  https://doi.org/10.2210/pdb5KDV/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2016-06-08 Released: 2017-01-11 
• Deposition Author(s): Noach, I., Boraston, A.B.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.204 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 

Literature

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

• PubMed: 28096352 
• 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; [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 98.97 kDa 
• Atom Count: 7,740 
• Modelled Residue Count: 891 
• Deposited Residue Count: 891 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metallopeptidase	A	891	Pseudomonas aeruginosa PAO1	Mutation(s): 1  Gene Names: PA0572, impA EC: 3.4.24
UniProt
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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	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]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 155.28	α = 90
b = 96.41	β = 124.66
c = 100.92	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-01-11 
Deposition Author(s): Noach, I., Boraston, A.B.

Revision History  

• 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