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4  structures 5738  species 0  interactions 28403  sequences 220  architectures

Family: FA_desaturase (PF00487)

Summary: Fatty acid desaturase

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Fatty acid desaturase". More...

Fatty acid desaturase Edit Wikipedia article

A Desaturase is an enzyme which removes two hydrogen atoms from an organic compound, creating a carbon/carbon double bond.

In the biosynthesis of essential fatty acids, different elongases alternate with desaturases (Δ6desaturase, Δ5desaturase, Δ4desaturase) repeatedly inserting an ethyl group, then forming a double bond.

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Fatty acid desaturase Provide feedback

Fatty acid desaturases are enzymes that catalyse the insertion of a double bond at the delta position of fatty acids. There seem to be two distinct families of fatty acid desaturases which do not seem to be evolutionary related: Family 1 composed of Stearoyl-CoA desaturases (SCD) [1,2] and Family 2 composed of Bacterial fatty acid desaturases, Plant stearoyl-acyl-carrier-protein desaturase [3] and Cyanobacterial DesA [4]. Members of this entry are ER integral membrane proteins that share the same mushroom-shaped fold consisting of four transmembrane helices (TM1-TM4) which anchor them to the membrane, capped by a cytosolic domain containing a unique 9-10 histidine- coordinating di metal (di-iron) catalytic centre [5,6]. The structure of mouse stearoyl-CoA desaturase (SDC) revealed that TM2 and TM4 are longer than TM1 and TM3 and protrude into the cytosolic domain, providing three of the nine histidine residues that coordinate the two metal ions, while the other histidine residues are provided by the soluble domain in this enzyme [5].

Literature references

  1. Lindqvist Y, Huang W, Schneider G, Shanklin J; , EMBO J 1996;15:4081-4092.: Crystal structure of delta9 stearoyl-acyl carrier protein desaturase from castor seed and its relationship to other di-iron proteins. PUBMED:8861937 EPMC:8861937

  2. Kaestner KH, Ntambi JM, Kelly TJ Jr, Lane MD;, J Biol Chem. 1989;264:14755-14761.: Differentiation-induced gene expression in 3T3-L1 preadipocytes. A second differentially expressed gene encoding stearoyl-CoA desaturase. PUBMED:2570068 EPMC:2570068

  3. Shanklin J, Somerville C;, Proc Natl Acad Sci U S A. 1991;88:2510-2514.: Stearoyl-acyl-carrier-protein desaturase from higher plants is structurally unrelated to the animal and fungal homologs. PUBMED:2006187 EPMC:2006187

  4. Wada H, Gombos Z, Murata N;, Nature. 1990;347:200-203.: Enhancement of chilling tolerance of a cyanobacterium by genetic manipulation of fatty acid desaturation. PUBMED:2118597 EPMC:2118597

  5. Shen J, Wu G, Tsai AL, Zhou M;, J Mol Biol. 2020;432:5152-5161.: Structure and Mechanism of a Unique Diiron Center in Mammalian Stearoyl-CoA Desaturase. PUBMED:32470559 EPMC:32470559

  6. Wang H, Klein MG, Zou H, Lane W, Snell G, Levin I, Li K, Sang BC;, Nat Struct Mol Biol. 2015;22:581-585.: Crystal structure of human stearoyl-coenzyme A desaturase in complex with substrate. PUBMED:26098317 EPMC:26098317


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005804

Fatty acid desaturases are enzymes that catalyse the insertion of a double bond at the delta position of fatty acids. There seem to be two distinct families of fatty acid desaturases which do not seem to be evolutionary related.

Family 1 is composed of:

Family 2 is composed of:

  • Bacterial fatty acid desaturases.
  • Plant stearoyl-acyl-carrier-protein desaturase ( EC ) [ PUBMED:2006187 ], this enzyme catalyzes the introduction of a double bond at the delta(9) position of steraoyl-ACP to produce oleoyl-ACP. This enzyme is responsible for the conversion of saturated fatty acids to unsaturated fatty acids in the synthesis of vegetable oils.
  • Cyanobacterial DesA [ PUBMED:2118597 ], an enzyme that can introduce a second cis double bond at the delta(12) position of fatty acid bound to membranes glycerolipids. DesA is involved in chilling tolerance; the phase transition temperature of lipids of cellular membranes being dependent on the degree of unsaturation of fatty acids of the membrane lipids.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan Acyl-CoA_desat (CL0713), which has the following description:

Families in this clan are integral membrane di-iron-containing enzymes that share the same fold consisting of four transmembrane helices (TM1-TM4) that anchor them to the endoplasmic reticulum (ER) membrane, capped by a cytosolic domain containing a unique 9-10 histidine-coordinating dimetal (di-iron) catalytic centre. This fold is found in fatty acid hydroxylases and fatty acid desaturases, which hydroxylate or desaturate lipid-based substrates in a NADH and oxygen-dependent reaction [1,2,3]. The structure of mouse stearoyl-CoA desaturase (SDC) revealed that TM2 and TM4 are longer than TM1 and TM3 and protrude into the cytosolic domain, providing three of the nine histidine residues that coordinate the two metal ions, while the other histidine residues are provided by the soluble domain in this enzyme [4].

The clan contains the following 3 members:

FA_desaturase FA_hydroxylase Lipid_desat

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(125)
Full
(28403)
Representative proteomes UniProt
(97121)
RP15
(4426)
RP35
(13233)
RP55
(26250)
RP75
(42419)
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PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(125)
Full
(28403)
Representative proteomes UniProt
(97121)
RP15
(4426)
RP35
(13233)
RP55
(26250)
RP75
(42419)
Alignment:
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Sequence:
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Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(125)
Full
(28403)
Representative proteomes UniProt
(97121)
RP15
(4426)
RP35
(13233)
RP55
(26250)
RP75
(42419)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Bateman A
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD , Bateman A
Number in seed: 125
Number in full: 28403
Average length of the domain: 242.4 aa
Average identity of full alignment: 15 %
Average coverage of the sequence by the domain: 64.45 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 29.7 29.7
Trusted cut-off 29.7 29.7
Noise cut-off 29.6 29.6
Model length: 254
Family (HMM) version: 27
Download: download the raw HMM for this family

Species distribution

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Selections

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the FA_desaturase domain has been found. There are 4 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A044T4N9 View 3D Structure Click here
A0A044TF45 View 3D Structure Click here
A0A044TTB7 View 3D Structure Click here
A0A077Z5R1 View 3D Structure Click here
A0A0A2V157 View 3D Structure Click here
A0A0D2DFF2 View 3D Structure Click here
A0A0D2DV32 View 3D Structure Click here
A0A0D2EYB1 View 3D Structure Click here
A0A0D2GQX0 View 3D Structure Click here
A0A0H3GPX6 View 3D Structure Click here
A0A0K0E4N0 View 3D Structure Click here
A0A0K0E6U6 View 3D Structure Click here
A0A0K0E6U7 View 3D Structure Click here
A0A0K0E7Q3 View 3D Structure Click here
A0A0K0EL94 View 3D Structure Click here
A0A0K0EN87 View 3D Structure Click here
A0A0K0JLR1 View 3D Structure Click here
A0A0N4U2U9 View 3D Structure Click here
A0A0P0XY37 View 3D Structure Click here
A0A0R0EN07 View 3D Structure Click here
A0A0R0F9U0 View 3D Structure Click here
A0A0R0HS17 View 3D Structure Click here
A0A0R0L7Y3 View 3D Structure Click here
A0A0R4J2X1 View 3D Structure Click here
A0A0R4J5W4 View 3D Structure Click here
A0A175W019 View 3D Structure Click here
A0A175W122 View 3D Structure Click here
A0A175W249 View 3D Structure Click here
A0A175W5J6 View 3D Structure Click here
A0A175W626 View 3D Structure Click here
A0A175WG81 View 3D Structure Click here
A0A1C1C725 View 3D Structure Click here
A0A1C1CAI2 View 3D Structure Click here
A0A1C1CQS6 View 3D Structure Click here
A0A1C1CWN4 View 3D Structure Click here
A0A1D6E4U5 View 3D Structure Click here
A0A1D6F511 View 3D Structure Click here
A0A1D6HT09 View 3D Structure Click here
A0A1D6IVG6 View 3D Structure Click here
A0A1D6JZ55 View 3D Structure Click here