Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 

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This is version 1.3 of the entry. See complete history


Crystal structure of PMGL2 esterase from the hormone-sensitive lipase family with GCSAG motif around the catalytic serine.

Boyko, K.M.Kryukova, M.V.Petrovskaya, L.E.Nikolaeva, A.Y.Korzhenevsky, D.A.Novototskaya-Vlasova, K.A.Rivkina, E.M.Dolgikh, D.A.Kirpichnikov, M.P.Popov, V.O.

(2020) PLoS One 15: e0226838-e0226838

  • DOI: https://doi.org/10.1371/journal.pone.0226838
  • Primary Citation of Related Structures:  
    6QIN, 6QLA

  • PubMed Abstract: 

    Lipases comprise a large class of hydrolytic enzymes which catalyze the cleavage of the ester bonds in triacylglycerols and find numerous biotechnological applications. Previously, we have cloned the gene coding for a novel esterase PMGL2 from a Siberian permafrost metagenomic DNA library. We have determined the 3D structure of PMGL2 which belongs to the hormone-sensitive lipase (HSL) family and contains a new variant of the active site motif, GCSAG. Similar to many other HSLs, PMGL2 forms dimers in solution and in the crystal. Our results demonstrated that PMGL2 and structurally characterized members of the GTSAG motif subfamily possess a common dimerization interface that significantly differs from that of members of the GDSAG subfamily of known structure. Moreover, PMGL2 had a unique organization of the active site cavity with significantly different topology compared to the other lipolytic enzymes from the HSL family with known structure including the distinct orientation of the active site entrances within the dimer and about four times larger size of the active site cavity. To study the role of the cysteine residue in GCSAG motif of PMGL2, the catalytic properties and structure of its double C173T/C202S mutant were examined and found to be very similar to the wild type protein. The presence of the bound PEG molecule in the active site of the mutant form allowed for precise mapping of the amino acid residues forming the substrate cavity.

  • Organizational Affiliation

    Department of Enzyme Engineering, Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
349permafrost metagenomeMutation(s): 0 
Find proteins for A0A142J6I6 (uncultured bacterium)
Explore A0A142J6I6 
Go to UniProtKB:  A0A142J6I6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A142J6I6
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.01α = 90
b = 92.35β = 106.83
c = 74.23γ = 90
Software Package:
Software NamePurpose
iMOSFLMdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Russian Foundation for Basic ResearchRussian Federation18-04-00491

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-25
    Type: Initial release
  • Version 1.1: 2020-02-19
    Changes: Database references
  • Version 1.2: 2021-08-11
    Changes: Database references, Derived calculations, Source and taxonomy
  • Version 1.3: 2024-01-24
    Changes: Data collection, Refinement description