7YGK | pdb_00007ygk

Crystal structure of a secretory phospholipase A2 from Sciscionella marina


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free: 
    0.197 (Depositor), 0.199 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.177 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structural and functional characterization of a thermostable secretory phospholipase A 2 from Sciscionella marina and its application in liposome biotransformation.

Kang, B.G.Kwon, S.Y.Lee, H.R.Hwang, Y.Youn, S.Y.Oh, C.Park, J.B.Cha, S.S.

(2023) Acta Crystallogr D Struct Biol 79: 188-197

  • DOI: https://doi.org/10.1107/S2059798323000384
  • Primary Citation Related Structures: 
    7YGK

  • PubMed Abstract: 

    Secretory phospholipase A 2 (sPLA 2 ), which hydrolyzes the sn-2 acyl bond of lecithin in a Ca 2+ -dependent manner, is an important enzyme in the oil and oleochemical industries. However, most sPLA 2 s are not stable under process conditions. Therefore, a thermostable sPLA 2 was investigated in this study. A marine bacterial sPLA 2 isolated from Sciscionella marina (Sm-sPLA 2 ) was catalytically active even after 5 h of incubation at high temperatures of up to 50°C, which is outstanding compared with a representative bacterial sPLA 2 (i.e. sPLA 2 from Streptomyces violaceoruber; Sv-sPLA 2 ). Consistent with this, the melting temperature of Sm-sPLA 2 was measured to be 7.7°C higher than that of Sv-sPLA 2 . Furthermore, Sm-sPLA 2 exhibited an improved biotransformation performance compared with Sv-sPLA 2 in the hydrolysis of soy lecithin to lysolecithin and free fatty acids at 50°C. Structural and mutagenesis studies revealed that the Trp41-mediated anchoring of a Ca 2+ -binding loop into the rest of the protein body is directly linked to the thermal stability of Sm-sPLA 2 . This finding provides a novel structural insight into the thermostability of sPLA 2 and could be applied to create mutant proteins with enhanced industrial potential.


  • Organizational Affiliation
    • Department of Chemistry and Nanoscience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Republic of Korea.

Macromolecule Content 

  • Total Structure Weight: 13.12 kDa 
  • Atom Count: 1,014 
  • Modeled Residue Count: 112 
  • Deposited Residue Count: 113 
  • Unique protein chains: 1

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
phospholipase A2113Sciscionella marinaMutation(s): 0 
UniProt
Find proteins for A0A9Y2YAE2 (Sciscionella marina)
Explore A0A9Y2YAE2 
Go to UniProtKB:  A0A9Y2YAE2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A9Y2YAE2
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free:  0.197 (Depositor), 0.199 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.177 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.38α = 90
b = 39.68β = 91.546
c = 54.3γ = 90
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-22
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-16
    Changes: Structure summary