1OGO | pdb_00001ogo

Dex49A from Penicillium minioluteum complex with isomaltose

• PDB DOI: https://doi.org/10.2210/pdb1OGO/pdb

• Classification: HYDROLASE
• Organism(s): Talaromyces minioluteus
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2003-05-08 Released: 2003-09-11 
• Deposition Author(s): Larsson, A.M., Stahlberg, J., Jones, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.215 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.199 (DCC) 

Literature

Dextranase from Penicillium Minioluteum. Reaction Course, Crystal Structure, and Product Complex

Larsson, A.M., Andersson, R., Stahlberg, J., Kenne, L., Jones, T.A.

(2003) Structure 11: 1111

• PubMed: 12962629 
• DOI: https://doi.org/10.1016/s0969-2126(03)00147-3
• Primary Citation Related Structures: 
  1OGM, 1OGO


• PubMed Abstract: 
  

  Dextranase catalyzes the hydrolysis of the alpha-1,6-glycosidic linkage in dextran polymers. The structure of dextranase, Dex49A, from Penicillium minioluteum was solved in the apo-enzyme and product-bound forms. The main domain of the enzyme is a right-handed parallel beta helix, which is connected to a beta sandwich domain at the N terminus. In the structure of the product complex, isomaltose was found to bind in a crevice on the surface of the enzyme. The glycosidic oxygen of the glucose unit in subsite +1 forms a hydrogen bond to the suggested catalytic acid, Asp395. By NMR spectroscopy the reaction course was shown to occur with net inversion at the anomeric carbon, implying a single displacement mechanism. Both Asp376 and Asp396 are suitably positioned to activate the water molecule that performs the nucleophilic attack. A new clan that links glycoside hydrolase families 28 and 49 is suggested.

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Organizational Affiliation: 
• Department of Cell and Molecular Biology, Biomedical Centre, University of Uppsala, Box 596, SE-751 24 Uppsala, Sweden.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 62.79 kDa 
• Atom Count: 4,929 
• Modeled Residue Count: 572 
• Deposited Residue Count: 574 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DEXTRANASE	A [auth X]	574	Talaromyces minioluteus	Mutation(s): 5  EC: 3.2.1.11
UniProt
Find proteins for P48845 (Talaromyces minioluteus) Explore P48845  Go to UniProtKB:  P48845

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-6)-beta-D-glucopyranose	B [auth A]	2		N/A
Glycosylation Resources
GlyTouCan: G45624LJ GlyCosmos: G45624LJ

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.215 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.199 (DCC) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.405	α = 90
b = 103.773	β = 90
c = 49.74	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MLPHARE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-09-11 
Deposition Author(s): Larsson, A.M., Stahlberg, J., Jones, T.A.

Revision History  

• Version 1.0: 2003-09-11
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-17
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2024-10-23
  Changes: Data collection, Database references, Structure summary