1T0O | pdb_00001t0o

The structure of alpha-galactosidase from Trichoderma reesei complexed with beta-D-galactose

• PDB DOI: https://doi.org/10.2210/pdb1T0O/pdb

• Classification: HYDROLASE
• Organism(s): Trichoderma reesei
• Mutation(s): No 


• Deposited: 2004-04-12 Released: 2004-10-12 
• Deposition Author(s): Golubev, A.M., Nagem, R.A.P., Brandao Neto, J.R., Neustroev, K.N., Eneyskaya, E.V., Kulminskaya, A.A., Shabalin, K.A., Savel'ev, A.N., Polikarpov, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 
  0.205 (Depositor) 
• R-Value Work: 
  0.151 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of alpha-galactosidase from Trichoderma reesei and its complex with galactose: implications for catalytic mechanism

Golubev, A.M., Nagem, R.A.P., Brandao Neto, J.R., Neustroev, K.N., Eneyskaya, E.V., Kulminskaya, A.A., Shabalin, K.A., Savel'ev, A.N., Polikarpov, I.

(2004) J Mol Biology 339: 413-422

• PubMed: 15136043 
• DOI: https://doi.org/10.1016/j.jmb.2004.03.062
• Primary Citation Related Structures: 
  1SZN, 1T0O


• PubMed Abstract: 
  

  The crystal structures of alpha-galactosidase from the mesophilic fungus Trichoderma reesei and its complex with the competitive inhibitor, beta-d-galactose, have been determined at 1.54 A and 2.0 A resolution, respectively. The alpha-galactosidase structure was solved by the quick cryo-soaking method using a single Cs derivative. The refined crystallographic model of the alpha-galactosidase consists of two domains, an N-terminal catalytic domain of the (beta/alpha)8 barrel topology and a C-terminal domain which is formed by an antiparallel beta-structure. The protein contains four N-glycosylation sites located in the catalytic domain. Some of the oligosaccharides were found to participate in inter-domain contacts. The galactose molecule binds to the active site pocket located in the center of the barrel of the catalytic domain. Analysis of the alpha-galactosidase- galactose complex reveals the residues of the active site and offers a structural basis for identification of the putative mechanism of the enzymatic reaction. The structure of the alpha-galactosidase closely resembles those of the glycoside hydrolase family 27. The conservation of two catalytic Asp residues, identified for this family, is consistent with a double-displacement reaction mechanism for the alpha-galactosidase. Modeling of possible substrates into the active site reveals specific hydrogen bonds and hydrophobic interactions that could explain peculiarities of the enzyme kinetics.

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Organizational Affiliation: 
• Petersburg Nuclear Physics Institute, Gatchina, St Petersburg, 188300, Russia.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 48.62 kDa 
• Atom Count: 3,798 
• Modeled Residue Count: 417 
• Deposited Residue Count: 417 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
alpha-galactosidase	A	417	Trichoderma reesei	Mutation(s): 0  EC: 3.2.1.22
UniProt
Find proteins for Q92456 (Hypocrea jecorina) Explore Q92456  Go to UniProtKB:  Q92456
Glycosylation
Glycosylation Sites: 4

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, E	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	C	7		N-Glycosylation
Glycosylation Resources
GlyTouCan: G55220VL GlyCosmos: G55220VL GlyGen: G55220VL

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
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	D	4		N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GAL	F [auth A]	beta-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free:  0.205 (Depositor) 
• R-Value Work:  0.151 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.834	α = 90
b = 58.313	β = 90
c = 153.66	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-10-12 
Deposition Author(s): Golubev, A.M., Nagem, R.A.P., Brandao Neto, J.R., Neustroev, K.N., Eneyskaya, E.V., Kulminskaya, A.A., Shabalin, K.A., Savel'ev, A.N., Polikarpov, I.

Revision History  

• Version 1.0: 2004-10-12
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-08-23
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-16
  Changes: Structure summary