8AKP

Crystal structure of the catalytic domain of G7048 from Penicillium sumatraense

• PDB DOI: https://doi.org/10.2210/pdb8AKP/pdb

• Classification: HYDROLASE
• Organism(s): Penicillium sumatraense
• Expression System: Komagataella pastoris DSMZ 70382
• Mutation(s): No 


• Deposited: 2022-07-30 Released: 2022-12-28 
• Deposition Author(s): Troilo, F., Scafati, V., Giovannoni, M., Mattei, B., Benedetti, M., Angelucci, F., Di Matteo, A.
• Funding Organization(s): Italian Ministry of Education

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.204 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 

Literature

Characterization of two 1,3-beta-glucan-modifying enzymes from Penicillium sumatraense reveals new insights into 1,3-beta-glucan metabolism of fungal saprotrophs.

Scafati, V., Troilo, F., Ponziani, S., Giovannoni, M., Scortica, A., Pontiggia, D., Angelucci, F., Di Matteo, A., Mattei, B., Benedetti, M.

(2022) Biotechnol Biofuels Bioprod 15: 138-138

• PubMed: 36510318 
• DOI: https://doi.org/10.1186/s13068-022-02233-8
• Primary Citation of Related Structures:  
  8AKP


• PubMed Abstract: 
  

  1,3-β-glucan is a polysaccharide widely distributed in the cell wall of several phylogenetically distant organisms, such as bacteria, fungi, plants and microalgae. The presence of highly active 1,3-β-glucanases in fungi evokes the biological question on how these organisms can efficiently metabolize exogenous sources of 1,3-β-glucan without incurring in autolysis.

---

Organizational Affiliation: 

Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100, L'Aquila, Italy.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: homology

Macromolecule Content

• Total Structure Weight: 32.44 kDa 
• Atom Count: 2,500 
• Modelled Residue Count: 288 
• Deposited Residue Count: 290 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
catalytic domain of G7048	A	290	Penicillium sumatraense	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	7		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G55220VL GlyCosmos:  G55220VL GlyGen:  G55220VL

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	C [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.204 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.22	α = 90
b = 87.3	β = 90
c = 42.53	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-12-28 
Deposition Author(s): Troilo, F., Scafati, V., Giovannoni, M., Mattei, B., Benedetti, M., Angelucci, F., Di Matteo, A.

---

Funding Organization	Location	Grant Number
Italian Ministry of Education	Italy	PRIN 2017ZBBYNC

Revision History  

• Version 1.0: 2022-12-28
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description