4ZR0

Full length scs7p (only hydroxylase domain visible)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.247 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The Crystal Structure of an Integral Membrane Fatty Acid alpha-Hydroxylase.

Zhu, G.Koszelak-Rosenblum, M.Connelly, S.M.Dumont, M.E.Malkowski, M.G.

(2015) J Biol Chem 290: 29820-29833

  • DOI: 10.1074/jbc.M115.680124
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Neuronal electrical impulse propagation is facilitated by the myelin sheath, a compact membrane surrounding the axon. The myelin sheath is highly enriched in galactosylceramide (GalCer) and its sulfated derivative sulfatide. Over 50% of GalCer and su ...

    Neuronal electrical impulse propagation is facilitated by the myelin sheath, a compact membrane surrounding the axon. The myelin sheath is highly enriched in galactosylceramide (GalCer) and its sulfated derivative sulfatide. Over 50% of GalCer and sulfatide in myelin is hydroxylated by the integral membrane enzyme fatty acid 2-hydroxylase (FA2H). GalCer hydroxylation contributes to the compact nature of the myelin membrane, and mutations in FA2H result in debilitating leukodystrophies and spastic paraparesis. We report here the 2.6 Å crystal structure of sphingolipid α-hydroxylase (Scs7p), a yeast homolog of FA2H. The Scs7p core is composed of a helical catalytic cap domain that sits atop four transmembrane helices that anchor the enzyme in the endoplasmic reticulum. The structure contains two zinc atoms coordinated by the side chains of 10 highly conserved histidines within a dimetal center located near the plane of the cytosolic membrane. We used a yeast genetic approach to confirm the important role of the dimetal-binding histidines in catalysis and identified Tyr-322 and Asp-323 as critical determinants involved in the hydroxylase reaction. Examination of the Scs7p structure, coupled with molecular dynamics simulations, allowed for the generation of a model of ceramide binding to Scs7p. Comparison of the Scs7p structure and substrate-binding model to the structure of steroyl-CoA desaturase revealed significant differences in the architecture of the catalytic cap domain and location of the dimetal centers with respect to the membrane. These observations provide insight into the different mechanisms of substrate binding and recognition of substrates by the hydroxylase and desaturase enzymes.


    Organizational Affiliation

    From the Hauptman-Woodward Medical Research Institute, Buffalo, New York 14203, the Department of Structural Biology, State University of New York at Buffalo, Buffalo, New York 14203 mgm22@buffalo.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ceramide very long chain fatty acid hydroxylase SCS7A, B392Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SCS7FAH1YMR272CYM8156.14C
EC: 1 (PDB Primary Data), 1.14.18.6 (UniProt), 1.14.18.7 (UniProt)
Find proteins for Q03529 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03529 
Go to UniProtKB:  Q03529
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.247 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 202.943α = 90
b = 202.943β = 90
c = 202.943γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU54 GM094611

Revision History 

  • Version 1.0: 2015-07-29
    Type: Initial release
  • Version 1.1: 2015-11-18
    Changes: Database references
  • Version 1.2: 2015-12-23
    Changes: Database references
  • Version 1.3: 2017-09-06
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.4: 2019-12-25
    Changes: Author supporting evidence