8B9S | pdb_00008b9s

NATIVE FORM, THERMOSTABLE LIPASE FROM THERMOANAEROBACTER THERMOHYDROSULFURICUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 
    0.255 (Depositor), 0.255 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery of a non-canonical prototype long-chain monoacylglycerol lipase through a structure-based endogenous reaction intermediate complex.

Pinotsis, N.Kruger, A.Tomas, N.Chatziefthymiou, S.D.Litz, C.Mortensen, S.A.Daffe, M.Marrakchi, H.Antranikian, G.Wilmanns, M.

(2023) Nat Commun 14: 7649-7649

  • DOI: https://doi.org/10.1038/s41467-023-43354-4
  • Primary Citation Related Structures: 
    7Q4H, 7Q4J, 8B9S

  • PubMed Abstract: 

    The identification and characterization of enzyme function is largely lacking behind the rapidly increasing availability of large numbers of sequences and associated high-resolution structures. This is often hampered by lack of knowledge on in vivo relevant substrates. Here, we present a case study of a high-resolution structure of an unusual orphan lipase in complex with an endogenous C18 monoacylglycerol ester reaction intermediate from the expression host, which is insoluble under aqueous conditions and thus not accessible for studies in solution. The data allowed its functional characterization as a prototypic long-chain monoacylglycerol lipase, which uses a minimal lid domain to position the substrate through a hydrophobic tunnel directly to the enzyme's active site. Knowledge about the molecular details of the substrate binding site allowed us to modulate the enzymatic activity by adjusting protein/substrate interactions, demonstrating the potential of our findings for future biotechnology applications.


  • Organizational Affiliation
    • European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607, Hamburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 176.34 kDa 
  • Atom Count: 12,661 
  • Modeled Residue Count: 1,554 
  • Deposited Residue Count: 1,554 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Prolyl oligopeptidase family protein
A, B, C, D, E
A, B, C, D, E, F
259Thermoanaerobacter ethanolicus subsp. thermohydrosulfuricusMutation(s): 0 
Gene Names: ThesiDRAFT1_1468
UniProt
Find proteins for A0A1G7VV58 (Thermoanaerobacter thermohydrosulfuricus)
Explore A0A1G7VV58 
Go to UniProtKB:  A0A1G7VV58
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1G7VV58
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D10
(Subject of Investigation/LOI)

Query on D10



Download:Ideal Coordinates CCD File
H [auth A]DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
J [auth B],
K [auth B],
M [auth D],
O [auth E],
P [auth E]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL

Query on GOL



Download:Ideal Coordinates CCD File
G [auth A],
I [auth B],
L [auth C],
N [auth E],
Q [auth F]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
K

Query on K



Download:Ideal Coordinates CCD File
R [auth F]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free:  0.255 (Depositor), 0.255 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.237α = 90
b = 125.237β = 90
c = 101.419γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
HKL-2000data reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-18
    Type: Initial release
  • Version 1.1: 2024-05-22
    Changes: Database references
  • Version 1.2: 2026-03-04
    Changes: Refinement description, Structure summary