1LGY | pdb_00001lgy

LIPASE II FROM RHIZOPUS NIVEUS

• PDB DOI: https://doi.org/10.2210/pdb1LGY/pdb

• Classification: HYDROLASE (CARBOXYLIC ESTER)
• Organism(s): Rhizopus niveus
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 1996-05-23 Released: 1996-12-23 
• Deposition Author(s): Kohno, M., Funatsu, J., Mikami, B., Kugimiya, W., Matsuo, T., Morita, Y.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Work: 
  0.186 (Depositor) 

Literature

The crystal structure of lipase II from Rhizopus niveus at 2.2 A resolution.

Kohno, M., Funatsu, J., Mikami, B., Kugimiya, W., Matsuo, T., Morita, Y.

(1996) J Biochem 120: 505-510

• PubMed: 8902613 
• DOI: https://doi.org/10.1093/oxfordjournals.jbchem.a021442
• Primary Citation Related Structures: 
  1LGY


• PubMed Abstract: 
  

  The crystal and molecular structure of Lipase II from Rhizopus niveus was analyzed using X-ray single crystal diffraction data at a resolution of 2.2 A. The structure was refined to an R-factor of 0.19 for all available data. This lipase was purified and crystallized as Lipase I, which contains two polypeptide chains combined through non-covalent interaction. However, during crystal growth, Lipase I was converted to Lipase II, which consists of a single polypeptide chain of 269 amino acid residues, by limited proteolysis. The structure of Lipase II shows a typical alpha/beta hydrolase fold containing the so-called nucleophilic elbow. The catalytic center of this enzyme is analogous to those of other neutral lipases and serine proteases. This catalytic center is sheltered by an alpha-helix lid, which appears in neutral lipases, opening the active site at the oil-water interface.

---

Organizational Affiliation: 
• Central Research Institute Tsukuba R&D Center, Fuji Oil Co., Ltd., Ibaraki. [e-mail]

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.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 88.87 kDa 
• Atom Count: 6,682 
• Modeled Residue Count: 795 
• Deposited Residue Count: 807 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRIACYLGLYCEROL LIPASE	A, B, C	269	Rhizopus niveus	Mutation(s): 0  EC: 3.1.1.3 Membrane Entity: Yes
UniProt
Find proteins for P61871 (Rhizopus niveus) Explore P61871  Go to UniProtKB:  P61871

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Work:  0.186 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.7	α = 90
b = 83.7	β = 90
c = 137.9	γ = 90

Software Package:

Software Name	Purpose
RIGAKU	data collection
X-PLOR	model building
TNT	refinement
X-PLOR	refinement
RIGAKU	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-12-23 
Deposition Author(s): Kohno, M., Funatsu, J., Mikami, B., Kugimiya, W., Matsuo, T., Morita, Y.

Revision History  

• Version 1.0: 1996-12-23
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-06-05
  Changes: Data collection, Database references, Other
• Version 1.4: 2024-10-30
  Changes: Structure summary