3O0D

Crystal structure of Lip2 lipase from Yarrowia lipolytica at 1.7 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Exploring the conformational states and rearrangements of Yarrowia lipolytica Lipase.

Bordes, F.Barbe, S.Escalier, P.Mourey, L.Andre, I.Marty, A.Tranier, S.

(2010) Biophys J 99: 2225-2234

  • DOI: https://doi.org/10.1016/j.bpj.2010.07.040
  • Primary Citation of Related Structures:  
    3O0D

  • PubMed Abstract: 

    We report the 1.7 Å resolution crystal structure of the Lip2 lipase from Yarrowia lipolytica in its closed conformation. The Lip2 structure is highly homologous to known structures of the fungal lipase family (Thermomyces lanuginosa, Rhizopus niveus, and Rhizomucor miehei lipases). However, it also presents some unique features that are described and discussed here in detail. Structural differences, in particular in the conformation adopted by the so-called lid subdomain, suggest that the opening mechanism of Lip2 may differ from that of other fungal lipases. Because the catalytic activity of lipases is strongly dependent on structural rearrangement of this mobile subdomain, we focused on elucidating the molecular mechanism of lid motion. Using the x-ray structure of Lip2, we carried out extensive molecular-dynamics simulations in explicit solvent environments (water and water/octane interface) to characterize the major structural rearrangements that the lid undergoes under the influence of solvent or upon substrate binding. Overall, our results suggest a two-step opening mechanism that gives rise first to a semi-open conformation upon adsorption of the protein at the water/organic solvent interface, followed by a further opening of the lid upon substrate binding.


  • Organizational Affiliation

    Université de Toulouse, Toulouse, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Triacylglycerol lipase
A, B, C, D, E
A, B, C, D, E, F, G
301Yarrowia lipolyticaMutation(s): 0 
Gene Names: lip2YALI0A20350g
EC: 3.1.1.3
Membrane Entity: Yes 
UniProt
Find proteins for Q9P8F7 (Yarrowia lipolytica)
Explore Q9P8F7 
Go to UniProtKB:  Q9P8F7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9P8F7
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
GA [auth E]
H [auth A]
HA [auth E]
AA [auth D],
BA [auth D],
GA [auth E],
H [auth A],
HA [auth E],
I [auth A],
LA [auth F],
MA [auth F],
O [auth B],
P [auth B],
QA [auth G],
RA [auth G],
U [auth C],
V [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MRD
Query on MRD

Download Ideal Coordinates CCD File 
DA [auth D],
M [auth A],
NA [auth F],
S [auth B]
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
MPD
Query on MPD

Download Ideal Coordinates CCD File 
CA [auth D]
EA [auth D]
IA [auth E]
J [auth A]
JA [auth E]
CA [auth D],
EA [auth D],
IA [auth E],
J [auth A],
JA [auth E],
K [auth A],
L [auth A],
OA [auth F],
Q [auth B],
R [auth B],
W [auth C],
X [auth C],
Y [auth C]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
K
Query on K

Download Ideal Coordinates CCD File 
FA [auth D]
KA [auth E]
N [auth A]
PA [auth F]
SA [auth G]
FA [auth D],
KA [auth E],
N [auth A],
PA [auth F],
SA [auth G],
T [auth B],
Z [auth C]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.354α = 90
b = 132.141β = 90
c = 137.255γ = 90
Software Package:
Software NamePurpose
DNAdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary