Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 66.92 kDa 
• Atom Count: 5155 
• Residue Count: 596 
• Unique protein chains: 2

4K90

Extracellular metalloproteinase from Aspergillus

• DOI: 10.2210/pdb4K90/pdb

• Classification: HYDROLASE
• Organism(s): Aspergillus fumigatus Af293
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2013-04-19 Released: 2013-10-23 
• Deposition Author(s): Fernandez, D., Russi, S., Vendrell, J., Monod, M., Pallares, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.198 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 

Literature

A functional and structural study of the major metalloprotease secreted by the pathogenic fungus Aspergillus fumigatus.

Fernandez, D., Russi, S., Vendrell, J., Monod, M., Pallares, I.

(2013) Acta Crystallogr D Biol Crystallogr 69: 1946-1957

• PubMed: 24100314 
• DOI: 10.1107/S0907444913017642
• Primary Citation of Related Structures:  
  4K90


• PubMed Abstract: 
  

Fungalysins are secreted fungal peptidases with the ability to degrade the extracellular matrix proteins elastin and collagen and are thought to act as virulence factors in diseases caused by fungi. Fungalysins constitute a unique family among zinc-dependent peptidases that bears low sequence similarity to known bacterial peptidases of the thermolysin family. The crystal structure of the archetype of the fungalysin family, Aspergillus fumigatus metalloprotease (AfuMep), has been obtained for the first time. The 1.8 Å resolution structure of AfuMep corresponds to that of an autoproteolyzed proenzyme with separate polypeptide chains corresponding to the N-terminal prodomain in a binary complex with the C-terminal zinc-bound catalytic domain. The prodomain consists of a tandem of cystatin-like folds whose C-terminal end is buried into the active-site cleft of the catalytic domain. The catalytic domain harbouring the key catalytic zinc ion and its ligands, two histidines and one glutamic acid, undergoes a conspicuous rearrangement of its N-terminal end during maturation. One key positively charged amino-acid residue and the C-terminal disulfide bridge appear to contribute to its structural-functional properties. Thus, structural, biophysical and biochemical analysis were combined to provide a deeper comprehension of the underlying properties of A. fumigatus fungalysin, serving as a framework for the as yet poorly known metallopeptidases from pathogenic fungi.

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Organizational Affiliation: 

Departament de Bioquímica i Biologia Molecular, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Extracellular metalloproteinase mep	A	389	Aspergillus fumigatus Af293	Mutation(s): 0  Gene Names: mep, AFUA_8G07080 EC: 3.4.24
Find proteins for P46075 (Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100)) Explore P46075  Go to UniProtKB:  P46075

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Extracellular metalloproteinase mep	B	215	Aspergillus fumigatus Af293	Mutation(s): 0  Gene Names: mep, AFUA_8G07080 EC: 3.4.24
Find proteins for P46075 (Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100)) Explore P46075  Go to UniProtKB:  P46075

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	3		N-Glycosylation

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLA	A	MALONIC ACID C3 H4 O4 OFOBLEOULBTSOW-UHFFFAOYSA-N
GOL	A, B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
BO3	A, B	BORIC ACID B H3 O3 KGBXLFKZBHKPEV-UHFFFAOYSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.198 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.398	α = 90
b = 85.398	β = 90
c = 176.092	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-04-19 
• Released Date: 2013-10-23 
Deposition Author(s): Fernandez, D., Russi, S., Vendrell, J., Monod, M., Pallares, I.

Revision History 

• Version 1.0: 2013-10-23
  Type: Initial release
  
• Version 1.1: 2015-04-29
  Changes: Structure summary
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary