3GCB | pdb_00003gcb

GAL6 (YEAST BLEOMYCIN HYDROLASE) MUTANT C73A/DELTAK454

• PDB DOI: https://doi.org/10.2210/pdb3GCB/pdb

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 1998-02-27 Released: 1998-10-21 
• Deposition Author(s): Joshua-Tor, L., Zheng, W., Johnston, S.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 
  0.217 (Depositor) 
• R-Value Work: 
  0.173 (Depositor) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

The unusual active site of Gal6/bleomycin hydrolase can act as a carboxypeptidase, aminopeptidase, and peptide ligase.

Zheng, W., Johnston, S.A., Joshua-Tor, L.

(1998) Cell 93: 103-109

• PubMed: 9546396 
• DOI: https://doi.org/10.1016/s0092-8674(00)81150-2
• Primary Citation Related Structures: 
  1A6R, 3GCB


• PubMed Abstract: 
  

  The Gal6 protease is in a class of cysteine peptidases identified by their ability to inactivate the anti-cancer drug bleomycin. The protein forms a barrel structure with the active sites embedded in a channel as in the proteasome. In Gal6 the C termini lie in the active site clefts. We show that Gal6 acts as a carboxypeptidase on its C terminus to convert itself to an aminopeptidase and peptide ligase. The substrate specificity of the peptidase activity is determined by the position of the C terminus of Gal6 rather than the sequence of the substrate. We propose a model to explain these diverse activities and Gal6's singular ability to inactivate bleomycin.

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Organizational Affiliation: 
• Center for Biomedical Inventions, Department of Medicine, University of Texas-Southwestern Medical Center, Dallas 75235-8573, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content 

• Total Structure Weight: 54.59 kDa 
• Atom Count: 4,152 
• Modeled Residue Count: 458 
• Deposited Residue Count: 470 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GAL6	A	470	Saccharomyces cerevisiae	Mutation(s): 1  Gene Names: GAL6C73ADELK EC: 3.4.22 (PDB Primary Data), 3.4.22.40 (UniProt)
UniProt
Find proteins for Q01532 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q01532  Go to UniProtKB:  Q01532

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free:  0.217 (Depositor) 
• R-Value Work:  0.173 (Depositor) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.547	α = 90
b = 150.547	β = 90
c = 90.134	γ = 120

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-10-21 
Deposition Author(s): Joshua-Tor, L., Zheng, W., Johnston, S.A.

Revision History  

• Version 1.0: 1998-10-21
  Type: Initial release
  
• Version 1.1: 2008-03-25
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2021-11-03
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-09
  Changes: Refinement description
• Version 1.5: 2024-05-22
  Changes: Data collection