Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 45.30 kDa 
• Atom Count: 3356 
• Modelled Residue Count: 371 
• Deposited Residue Count: 398 
• Unique protein chains: 1

2Y6U

Peroxisomal alpha-beta-hydrolase Lpx1 (Yor084w) from Saccharomyces cerevisiae (crystal form II)

• PDB DOI: 10.2210/pdb2Y6U/pdb

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-01-26 Released: 2011-07-13 
• Deposition Author(s): Thoms, S., Niemann, H.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.179 
• R-Value Work: 0.153 
• R-Value Observed: 0.155 

Literature

The Unusual Extended C-Terminal Helix of the Peroxisomal Alpha-Beta-Hydrolase Lpx1 is Involved in Dimer Contacts But Dispensable for Dimerization

Thoms, S., Hofhuis, J., Thoing, C., Gartner, J., Niemann, H.H.

(2011) J Struct Biol 175: 362

• PubMed: 21741480 
• DOI: 10.1016/j.jsb.2011.06.008
• Primary Citation of Related Structures:  
  2Y6U, 2Y6V


• PubMed Abstract: 
  

The yeast peroxisomal hydrolase Lpx1 belongs to the α/β-hydrolase superfamily. In the absence of Lpx1, yeast peroxisomes show an aberrant vacuolated morphology similar to what is found in peroxisomal disorder patients. Here, we present the crystal structure of Lpx1 determined at a resolution of 1.9 Å. The structure reveals the complete catalytic triad with an unusual location of the acid residue after strand β6 of the canonical α/β-hydrolase fold. A four-helix cap domain covers the active site. The interface between the α/β-hydrolase core and the cap domain forms the potential substrate binding site, which may also comprise the tunnel that leads into the protein interior and widens into a cavity. Two further tunnels connect the active site to the protein surface, potentially facilitating substrate access. Lpx1 is a homodimer. The α/β-hydrolase core folds of the two protomers form the dimer contact site. Further dimerization contacts arise from the mutual embracement of the cap domain of one protomer by the non-canonical C-terminal helix of the other, resulting in a total buried surface area of some 6000 Ų. The unusual C-terminal helix sticks out from the core fold to which it is connected by an extended flexible loop. We analyzed whether this helix is required for dimerization and for import of the dimer into peroxisomes using biochemical assays in vitro and a microscopy-based interaction assay in mammalian cells. Surprisingly, the C-terminal helix is dispensable for dimerization and dimer import. The unusually robust self-interaction suggests that Lpx1 is imported into peroxisomes as dimer.

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Organizational Affiliation: 

Department of Pediatrics and Pediatric Neurology, University Medical Center, University of Göttingen, Robert-Koch-Str. 40, 37075 Göttingen, Germany. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEROXISOMAL MEMBRANE PROTEIN LPX1	A	398	Saccharomyces cerevisiae	Mutation(s): 0  EC: 3.1.1
UniProt
Find proteins for Q12405 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12405  Go to UniProtKB:  Q12405

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.179 
• R-Value Work: 0.153 
• R-Value Observed: 0.155 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.156	α = 90
b = 87.156	β = 90
c = 125.52	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-01-26 
• Released Date: 2011-07-13 
Deposition Author(s): Thoms, S., Niemann, H.H.

Revision History  

• Version 1.0: 2011-07-13
  Type: Initial release
  
• Version 1.1: 2011-08-17
  Changes: Database references
• Version 1.2: 2019-07-24
  Changes: Data collection, Derived calculations
• Version 1.3: 2019-09-25
  Changes: Data collection, Experimental preparation, Other