4DOT | pdb_00004dot

Crystal structure of human HRASLS3.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 
    0.216 (Depositor), 0.238 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4DOT

This is version 1.2 of the entry. See complete history

Literature

Structural Basis for the Acyltransferase Activity of Lecithin:Retinol Acyltransferase-like Proteins.

Golczak, M.Kiser, P.D.Sears, A.E.Lodowski, D.T.Blaner, W.S.Palczewski, K.

(2012) J Biological Chem 287: 23790-23807

  • DOI: https://doi.org/10.1074/jbc.M112.361550
  • Primary Citation Related Structures: 
    4DOT, 4DPZ

  • PubMed Abstract: 

    Lecithin:retinol acyltransferase-like proteins, also referred to as HRAS-like tumor suppressors, comprise a vertebrate subfamily of papain-like or NlpC/P60 thiol proteases that function as phospholipid-metabolizing enzymes. HRAS-like tumor suppressor 3, a representative member of this group, plays a key role in regulating triglyceride accumulation and energy expenditure in adipocytes and therefore constitutes a novel pharmacological target for treatment of metabolic disorders causing obesity. Here, we delineate a catalytic mechanism common to lecithin:retinol acyltransferase-like proteins and provide evidence for their alternative robust lipid-dependent acyltransferase enzymatic activity. We also determined high resolution crystal structures of HRAS-like tumor suppressor 2 and 3 to gain insight into their active site architecture. Based on this structural analysis, two conformational states of the catalytic Cys-113 were identified that differ in reactivity and thus could define the catalytic properties of these two proteins. Finally, these structures provide a model for the topology of these enzymes and allow identification of the protein-lipid bilayer interface. This study contributes to the enzymatic and structural understanding of HRAS-like tumor suppressor enzymes.


  • Organizational Affiliation
    • Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA. mxg149@case.edu

Macromolecule Content 

  • Total Structure Weight: 15.9 kDa 
  • Atom Count: 884 
  • Modeled Residue Count: 102 
  • Deposited Residue Count: 140 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Group XVI phospholipase A2140Homo sapiensMutation(s): 0 
Gene Names: PLA2G16HRASLS3HREV107
EC: 3.1.1 (PDB Primary Data), 2.3.1 (UniProt), 3.1.1.4 (UniProt), 3.1.1.32 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P53816 (Homo sapiens)
Explore P53816 
Go to UniProtKB:  P53816
PHAROS:  P53816
GTEx:  ENSG00000176485 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53816
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free:  0.216 (Depositor), 0.238 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.446α = 90
b = 62.446β = 90
c = 73.922γ = 120
Software Package:
Software NamePurpose
XDSdata scaling
SHARPphasing
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-30
    Type: Initial release
  • Version 1.1: 2012-07-25
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references