PDBsum entry 4zr1

Oxidoreductase

PDB id: 4zr1

Contents

Protein chains

274 a.a.

Ligands

BOG ×8

TRD ×8

Metals

_ZN ×4

PDB id:

4zr1

Name:

Oxidoreductase

Title:

Hydroxylase domain of scs7p

Structure:

Ceramide very long chain fatty acid hydroxylase scs7. Chain: a, b. Fragment: unp residues 96-384. Synonym: ceramide vlcfa hydroxylase scs7,suppressor of calcium sensitivity 7. Engineered: yes

Source:

Saccharomyces cerevisiae (strain atcc 204508 / s288c). Baker's yeast. Organism_taxid: 559292. Strain: atcc 204508 / s288c. Gene: scs7, fah1, ymr272c, ym8156.14c. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932.

Resolution:

2.60Å R-factor: 0.199 R-free: 0.239

Authors:

G.Zhu,M.Koszelak-Rosenblum,M.G.Malkowski,Membrane Protein Structural Biology Consortium (Mpsbc)

Key ref:

G.Zhu et al. (2015). The Crystal Structure of an Integral Membrane Fatty Acid α-Hydroxylase. J Biol Chem, 290, 29820-29833. PubMed id: 26515067 DOI: 10.1074/jbc.M115.680124

Date:

11-May-15 Release date: 29-Jul-15

Protein chains

Q03529  (SCS7_YEAST) -  Ceramide very long chain fatty acid hydroxylase SCS7 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 384 a.a.

Struc: 274 a.a.

Enzyme reactions

• Enzyme class 1: E.C.1.14.18.6 - 4-hydroxysphinganine ceramide fatty acyl 2-hydroxylase.
• Reaction:
  1. an N-(1,2 saturated acyl)-(4R)-hydroxysphinganine + 2 Fe(II)- [cytochrome b5] + O2 + 2 H⁺ = an N-(2R-hydroxyacyl)- 4R-hydroxysphinganine + 2 Fe(III)-[cytochrome b5] + H2O
  2. an N-(1,2 saturated very-long-chain fatty acyl)-(R)-4- hydroxysphingoid base + 2 Fe(II)-[cytochrome b5] + O2 + 2 H⁺ = an N-(2R-hydroxy-very-long-chain fatty acyl)-(R)-4-hydroxysphingoid base + 2 Fe(III)-[cytochrome b5] + H2O
• Enzyme class 2: E.C.1.14.18.7 - dihydroceramide fatty acyl 2-hydroxylase.
• Reaction: an N-(1,2-saturated acyl)sphinganine + 2 Fe(II)-[cytochrome b5] + O2 + 2 H⁺ = an N-[(2'R)-hydroxyacyl]sphinganine + 2 Fe(III)-[cytochrome b5] + H2O

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1074/jbc.M115.680124

J Biol Chem 290:29820-29833 (2015)

PubMed id: 26515067

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

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

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 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.