3UUE

Crystal structure of mono- and diacylglycerol lipase from Malassezia globosa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 

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This is version 2.0 of the entry. See complete history


Literature

Crystal structure of a mono- and diacylglycerol lipase from Malassezia globosa reveals a novel lid conformation and insights into the substrate specificity.

Xu, T.Liu, L.Hou, S.Xu, J.Yang, B.Wang, Y.Liu, J.

(2012) J Struct Biol 178: 363-369

  • DOI: 10.1016/j.jsb.2012.03.006
  • Primary Citation of Related Structures:  
    3UUE, 3UUF

  • PubMed Abstract: 
  • Most lipases contain a lid domain to shield the hydrophobic binding site from the water environment. The lid, mostly in helical form, can undergo a conformational change to expose the active cleft during the interfacial activation. Here we report the crystal structures of Malassezia globosa LIP1 (SMG1) at 1 ...

    Most lipases contain a lid domain to shield the hydrophobic binding site from the water environment. The lid, mostly in helical form, can undergo a conformational change to expose the active cleft during the interfacial activation. Here we report the crystal structures of Malassezia globosa LIP1 (SMG1) at 1.45 and 2.60 Å resolution in two crystal forms. The structures present SMG1 in its closed form, with a novel lid in loop conformation. SMG1 is one of the few members in the fungal lipase family that has been found to be strictly specific for mono- and diacylglycerol. To date, the mechanism for this substrate specificity remains largely unknown. To investigate the substrate binding properties, we built a model of SMG1 in open conformation. Based on this model, we found that the two bulky hydrophobic residues adjacent to the catalytic site and the N-terminal hinge region of the lid both may act as steric hindrances for triacylglycerols binding. These unique structural features of SMG1 will provide a better understanding on the substrate specificity of mono- and diacylglycerol lipases and a platform for further functional study of this enzyme.


    Organizational Affiliation

    School of Life Sciences, University of Science and Technology of China, Hefei 230026, People's Republic of China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LIP1, secretory lipase (Family 3)A279Malassezia globosa CBS 7966Mutation(s): 0 
Gene Names: MGL_0797
UniProt
Find proteins for A8PUY1 (Malassezia globosa (strain ATCC MYA-4612 / CBS 7966))
Explore A8PUY1 
Go to UniProtKB:  A8PUY1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8PUY1
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB 5N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G10756ZZ
GlyCosmos:  G10756ZZ
GlyGen:  G10756ZZ
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download Ideal Coordinates CCD File 
C [auth A]alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.807α = 90
b = 88.744β = 106.04
c = 45.132γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-04-25
    Type: Initial release
  • Version 1.1: 2013-07-17
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary