2CZQ | pdb_00002czq

A novel cutinase-like protein from Cryptococcus sp.

• PDB DOI: https://doi.org/10.2210/pdb2CZQ/pdb

• Classification: HYDROLASE
• Organism(s): Cryptococcus sp. S-2
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2005-07-14 Released: 2006-07-14 
• Deposition Author(s): Masaki, K., Kamini, N.R., Ikeda, H., Iefuji, H., Kondo, H., Suzuki, M., Tsuda, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 
  0.157 (Depositor), 0.162 (DCC) 
• R-Value Work: 
  0.147 (Depositor), 0.153 (DCC) 
• R-Value Observed: 
  0.148 (Depositor) 

Literature

Crystal structure and enhanced activity of a cutinase-like enzyme from Cryptococcus sp. strain S-2

Kodama, Y., Masaki, K., Kondo, H., Suzuki, M., Tsuda, S., Nagura, T., Shimba, N., Suzuki, E., Iefuji, H.

(2009) Proteins 77: 710-717

• PubMed: 19544571 
• DOI: https://doi.org/10.1002/prot.22484
• Primary Citation Related Structures: 
  2CZQ


• PubMed Abstract: 
  

  The structural and enzymatic characteristics of a cutinase-like enzyme (CLE) from Cryptococcus sp. strain S-2, which exhibits remote homology to a lipolytic enzyme and a cutinase from the fungus Fusarium solani (FS cutinase), were compared to investigate the unique substrate specificity of CLE. The crystal structure of CLE was solved to a 1.05 A resolution. Moreover, hydrolysis assays demonstrated the broad specificity of CLE for short and long-chain substrates, as well as the preferred specificity of FS cutinase for short-chain substrates. In addition, site-directed mutagenesis was performed to increase the hydrolysis activity on long-chain substrates, indicating that the hydrophobic aromatic residues are important for the specificity to the long-chain substrate. These results indicate that hydrophobic residues, especially the aromatic ones exposed to solvent, are important for retaining lipase activity.

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Organizational Affiliation: 
• Institute of Life Sciences, Ajinomoto Co., Inc., Kawasaki-ku, Kawasaki-shi 210-8681, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 42.37 kDa 
• Atom Count: 3,451 
• Modeled Residue Count: 410 
• Deposited Residue Count: 410 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cutinase-like protein	A, B	205	Cryptococcus sp. S-2	Mutation(s): 0  EC: 3.1.1 Membrane Entity: Yes
UniProt
Find proteins for Q874E9 (Cryptococcus sp. S-2) Explore Q874E9  Go to UniProtKB:  Q874E9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	C [auth A], E [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
EDO	D [auth A], F [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free:  0.157 (Depositor), 0.162 (DCC) 
• R-Value Work:  0.147 (Depositor), 0.153 (DCC) 
• R-Value Observed: 0.148 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.478	α = 90
b = 82.807	β = 90
c = 123.514	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
CCP4	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-07-14 
Deposition Author(s): Masaki, K., Kamini, N.R., Ikeda, H., Iefuji, H., Kondo, H., Suzuki, M., Tsuda, S.

Revision History  

• Version 1.0: 2006-07-14
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2012-06-13
  Changes: Database references
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary