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1 Stearoyl-CoA Desaturase 1 from Mus musculus
2 Active Site
3 References
4 Student Contributors

Stearoyl-CoA Desaturase 1 from Mus musculus

This is a default text for your page Josey McKinley/Sandbox 1. Click above on edit this page to modify. Be careful with the < and > signs.

You may include any references to papers as in: the use of JSmol in Proteopedia ^[1] or to the article describing Jmol ^[2] to the rescue.

1 Introduction
2 Binding of the Substrate
3 Function
4 Disease
5 Relevance
6 Structural highlights

Introduction

Stearoyl-CoA Desaturase 1 (SCD1) is an iron-containing Δ-9-desaturase that is a key regulator of fatty-acid metabolism where it catalyzes the rate-limiting step in the conversion of Stearoyl-CoA to oleic acid, an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol. SCD1 is embedded within the membrane of the endoplasmic reticulum and consists of 4 transmembrane alpha helices and 11 cytosolic helices.

Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a dehydrogenation reaction between the of Stearoyl-CoA. This reaction is catalyzed by two iron ions that reside within the catalytic center of SCD1 which are oriented by 8 essential histidine residues.

Mechanistically, this reaction involves a molecular oxygen, water molecule, and the transport of electrons down an electron transport chain consisting of cytochrome b5 reductase, cytochrome b5, and NADH to the irons ions within SCD1 which then through a series of redox reactions introduces a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid.

SCD stands for Stearoyl-CoA Desaturase. This enzyme is highly conserved in eukaryotes and has different isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD discussed in this page is the SCD-1 found in mice. SCD was thought to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography. This enzyme is embedded in the membrane of the Endoplasmic Reticulum. SCD is made up of 15 alpha helices; four helices are embedded in the membrane and 11 helices in the cytosol. The substrate binds to the helices in the cytosol.

Binding of the Substrate

Stearoyl-CoA is the substrate that binds to the enzyme, SCD1. The binding of the substrate is stabilized by specific residues on the exterior and interior of the protein. Stearoyl-CoA is a long-chain fatty acyl-CoA. The head group of the substrate is composed of an adenine, ribose, phosphate groups, and many atoms of Nitrogen, oxygen, and sulfur. The fatty acid tail is a 17-carbon chain which reaches into the interior of the protein. The head of stearoyl-CoA is attached to the exterior of the protein by polar residues. The adenine, ribose, and phosphate are attached via groups that include R151, D152, and K185. The rest of the exterior of the substrate is attached via groups that include R184, N144, and N71. The fatty acid chain dives into the interior of the enzyme. The acyl chain is enclosed in a tunnel (24 ang) buried in the cytosolic domain. The geometry of the tunnel and formation of bound acyl chain are the structural basis for the stereospecificity of the desaturation reaction. The chain is kinked at carbon 9-carbon 10 where the double bond is generated. The is induced through the interactions of four conserved residues. Three out of four of these residues are not bound to the chain, but are hydrogen bonded to each other: . T257 is hydrogen bonded to Q143, and Q143 is hydrogen bonded to W149. These residues are directly below the kink and will be hydrolyzed when the substrate is ready to be released. The residue that is directly hydrogen bonded to the chain is . This residue is highly conserved and stabilizes the chain so it will be in the correct orientation in the active site.

Function

Disease

Relevance

Structural highlights

Active Site

Two structures of SCD known. One structure shows the substrate, water molecule, and zinc (4YMK). The second structure shows the product and iron (6WF2). For the pictures below, the structure is shown with two zinc ions in order to demonstrate how is coordination with the ions. Water is used in the mechanism, which is why we chose to use the structure with zinc to explain the active site. The two are 6.4 Angstroms apart. The ions sit above the kink in the active site. They are stabilized by the . The ion closest to C9 is 5.2 angstroms from it. This ion interacts with 4 histidines, H156, H265, H294, H298, and one water molecule. The ion closest to C10 is 4.7 angstroms away from it. This ion interacts with 5 histidines, H116, H121, H153, H157, and H297. These 9 total Histidine residues form a .The his box is used to stabilize the ions into the active site, forming a prosthetic group. The his box is highly conserved among the other isoforms of SCD. Other residues around the his box are used to hydrogen bond to the histidines to stabilize them. These residues include: ,

,, and

References

^[3]

↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644
↑ Ransey E, Paredes E, Dey SK, Das SR, Heroux A, Macbeth MR. Crystal structure of the Entamoeba histolytica RNA lariat debranching enzyme EhDbr1 reveals a catalytic Zn(2+) /Mn(2+) heterobinucleation. FEBS Lett. 2017 Jul;591(13):2003-2010. doi: 10.1002/1873-3468.12677. Epub 2017, Jun 14. PMID:28504306 doi:http://dx.doi.org/10.1002/1873-3468.12677

Student Contributors

Josey McKinley
Abbey Wells
Anthony Durand

Proteopedia Page Contributors and Editors (what is this?)

Josey McKinley

Retrieved from "http://52.214.119.220/wiki/index.php/User:Josey_McKinley/Sandbox_1"

@@ Line 1: / Line 1: @@
 ==Stearoyl-CoA Desaturase 1 from ''Mus musculus''==
-<StructureSection load='4ymk' size='350' frame='true' side='right' caption='Stearoyl-CoA Desaturase 1- 4YMK' scene=’’>='right' caption='Caption for this structure' scene=''>
+<StructureSection load='6WF2' size='350' frame = 'true' side='right' caption='Structure of SCD1' scene='87/877606/Introduction-di-iron-image/1'>
 This is a default text for your page '''Josey McKinley/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.
 You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.
@@ Line 6: / Line 6: @@
 == Introduction==
+[http://en.wikipedia.org/wiki/Stearoyl-CoA_desaturase-1 Stearoyl-CoA Desaturase 1 (SCD1)] is an iron-containing [http://en.wikipedia.org/wiki/Fatty_acid_desaturase Δ-9-desaturase]  that is a key regulator of fatty-acid metabolism where it catalyzes the rate-limiting step in the conversion of [http://en.wikipedia.org/wiki/Stearoyl-CoA Stearoyl-CoA] to [http://en.wikipedia.org/wiki/Oleic_acid oleic acid], an essential substrate in the biosynthesis of phospholipids, triacyclglycerols, and cholesterol. SCD1 is embedded within the membrane of the [http://micro.magnet.fsu.edu/cells/endoplasmicreticulum/endoplasmicreticulum.html endoplasmic reticulum] and consists of 4 transmembrane alpha helices and 11 cytosolic helices.
+Its substrate, Stearoyl-CoA, binds to the cytosolic region which contains a "kink" that properly orients Stearoyl-CoA to undergo a [http://en.wikipedia.org/wiki/Dehydrogenation#:~:text=Dehydrogenation%20is%20the%20a%20chemical,reaction%20and%20a%20serious%20problem.&text=Enzymes%20that%20catalyze%20dehydrogenation%20are%20called%20dehydrogenases. dehydrogenation] reaction between the <scene name='87/877606/Ligand-highlighted/3'>9th and 10th carbons</scene> of Stearoyl-CoA. This reaction is catalyzed by two iron ions that reside within the catalytic center of SCD1 which are oriented by 8 essential histidine residues.
+Mechanistically, this reaction involves a molecular oxygen, water molecule, and the transport of electrons down an [http://en.wikipedia.org/wiki/Electron_transport_chain electron transport chain] consisting of cytochrome b5 reductase, cytochrome b5, and NADH to the irons ions within SCD1 which then through a series of redox reactions introduces a double bond between the 9th and 10th carbons of Stearoyl-CoA forming oleic acid.
 SCD stands for Stearoyl-CoA Desaturase. This enzyme is highly conserved in eukaryotes and has different isoforms. Mice have four isoforms: SCD1, SCD2, SCD3, and SCD4. Humans have two different isoforms: SCD1 and SCD5. The SCD discussed in this page is the SCD-1 found in mice. SCD was thought to have once been an anaerobic pathway found in cartilaginous fish about 450 million years ago. The enzyme’s mechanism is now aerobic and this aerobic pathway is favored. The structure of SCD1 was found using X-ray crystallography. This enzyme is embedded in the membrane of the Endoplasmic Reticulum. SCD is made up of 15 alpha helices; four helices are embedded in the membrane and 11 helices in the cytosol. The substrate binds to the helices in the cytosol.