6A12 | pdb_00006a12

X-ray structure of lipase from Geobacillus thermoleovorans

• PDB DOI: https://doi.org/10.2210/pdb6A12/pdb

• Classification: HYDROLASE
• Organism(s): Geobacillus thermoleovorans
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-06-06 Released: 2018-06-20 
• Deposition Author(s): Moharana, T.R., Pal, B., Rao, N.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.221 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

X-ray structure and characterization of a thermostable lipase from Geobacillus thermoleovorans.

Moharana, T.R., Pal, B., Rao, N.M.

(2019) Biochem Biophys Res Commun 508: 145-151

• PubMed: 30471860 
• DOI: https://doi.org/10.1016/j.bbrc.2018.11.105
• Primary Citation Related Structures: 
  6A12


• PubMed Abstract: 
  

  Thermo-alkalophilic bacterium, Geobacillus thermoleovorans secrets many enzymes including a 43 kDa extracellular lipase. Significant thermostability, organic solvent stability and wide substrate preferences for hydrolysis drew our attention to solve its structure by crystallography. The structure was solved by molecular replacement method and refined up to 2.14 Å resolution. Structure of the lipase showed an alpha-beta fold with 19 α-helices and 10 β-sheets. The active site remains covered by a lid. One calcium and one zinc atom was found in the crystal. The structure showed a major difference (rmsd 5.6 Å) from its closest homolog in the amino acid region 191 to 203. Thermal unfolding of the lipase showed that the lipase is highly stable with T _m of 76 °C. ¹³ C NMR spectra of products upon triglyceride hydrolysate revealed that the lipase hydrolyses at both sn-1 and sn-2 positions with equal efficiency.

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Organizational Affiliation: 
• CSIR- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India.
CSIR- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India. Electronic address: [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 43.43 kDa 
• Atom Count: 3,160 
• Modeled Residue Count: 386 
• Deposited Residue Count: 389 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipase	A	389	Geobacillus thermoleovorans	Mutation(s): 0  Gene Names: lipA EC: 3.1.1.3
UniProt
Find proteins for Q8L1V2 (Geobacillus thermoleovorans) Explore Q8L1V2  Go to UniProtKB:  Q8L1V2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.221 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.14	α = 90
b = 72.291	β = 90
c = 112.405	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-06-20 
Deposition Author(s): Moharana, T.R., Pal, B., Rao, N.M.

Revision History  

• Version 1.0: 2018-06-20
  Type: Initial release
  
• Version 1.1: 2019-01-16
  Changes: Data collection, Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description