Summary: Enoyl-CoA hydratase/isomerase family
This is the Wikipedia entry entitled "Crotonase family". More...
The Wikipedia text that you see displayed here is a download from Wikipedia. This means that the information we display is a copy of the information from the Wikipedia database. The button next to the article title ("Edit Wikipedia article") takes you to the edit page for the article directly within Wikipedia. You should be aware you are not editing our local copy of this information. Any changes that you make to the Wikipedia article will not be displayed here until we next download the article from Wikipedia. We currently download new content on a nightly basis.
Does Pfam agree with the content of the Wikipedia entry ?
Pfam has chosen to link families to Wikipedia articles. In some case we have created or edited these articles but in many other cases we have not made any direct contribution to the content of the article. The Wikipedia community does monitor edits to try to ensure that (a) the quality of article annotation increases, and (b) vandalism is very quickly dealt with. However, we would like to emphasise that Pfam does not curate the Wikipedia entries and we cannot guarantee the accuracy of the information on the Wikipedia page.
Editing Wikipedia articles
Before you edit for the first time
Wikipedia is a free, online encyclopedia. Although anyone can edit or contribute to an article, Wikipedia has some strong editing guidelines and policies, which promote the Wikipedia standard of style and etiquette. Your edits and contributions are more likely to be accepted (and remain) if they are in accordance with this policy.
You should take a few minutes to view the following pages:
How your contribution will be recorded
Anyone can edit a Wikipedia entry. You can do this either as a new user or you can register with Wikipedia and log on. When you click on the "Edit Wikipedia article" button, your browser will direct you to the edit page for this entry in Wikipedia. If you are a registered user and currently logged in, your changes will be recorded under your Wikipedia user name. However, if you are not a registered user or are not logged on, your changes will be logged under your computer's IP address. This has two main implications. Firstly, as a registered Wikipedia user your edits are more likely seen as valuable contribution (although all edits are open to community scrutiny regardless). Secondly, if you edit under an IP address you may be sharing this IP address with other users. If your IP address has previously been blocked (due to being flagged as a source of 'vandalism') your edits will also be blocked. You can find more information on this and creating a user account at Wikipedia.
If you have problems editing a particular page, contact us at email@example.com and we will try to help.
The community annotation is a new facility of the Pfam web site. If you have problems editing or experience problems with these pages please contact us.
Crotonase family Edit Wikipedia article
|Enoyl-CoA hydratase/isomerase family|
The crotonase family comprises mechanistically diverse proteins that share a conserved trimeric quaternary structure (sometimes a hexamer consisting of a dimer of trimers), the core of which consists of 4 turns of a (beta/beta/alpha)n superhelix.
Some enzymes in the superfamily have been shown to display dehalogenase, hydratase, and isomerase activities, while others have been implicated in carbon-carbon bond formation and cleavage as well as the hydrolysis of thioesters. However, these different enzymes share the need to stabilize an enolate anion intermediate derived from an acyl-CoA substrate. This is accomplished by two structurally conserved peptidic NH groups that provide hydrogen bonds to the carbonyl moieties of the acyl-CoA substrates and form an "oxyanion hole". The CoA thioester derivatives bind in a characteristic hooked shape and a conserved tunnel binds the pantetheine group of CoA, which links the 3'-phosphate ADP binding site to the site of reaction. Enzymes in the crotonase superfamily include:
- Enoyl-CoA hydratase (crotonase; EC 220.127.116.11), which catalyses the hydratation of 2-trans-enoyl-CoA into 3-hydroxyacyl-CoA.
- 3-2trans-enoyl-CoA isomerase (or dodecenoyl-CoA isomerise; EC 18.104.22.168), which shifts the 3-double bond of the intermediates of unsaturated fatty acid oxidation to the 2-trans position.
- 3-hydroxbutyryl-CoA dehydratase (crotonase; EC 22.214.171.124), a bacterial enzyme involved in the butyrate/butanol-producing pathway.
- 4-Chlorobenzoyl-CoA dehalogenase (EC 126.96.36.199), a Pseudomonas enzyme which catalyses the conversion of 4-chlorobenzoate-CoA to 4-hydroxybenzoate-CoA.
- Dienoyl-CoA isomerase, which catalyses the isomerisation of 3-trans,5-cis-dienoyl-CoA to 2-trans,4-trans-dienoyl-CoA.
- Naphthoate synthase (MenB, or DHNA synthetase; EC 188.8.131.52), a bacterial enzyme involved in the biosynthesis of menaquinone (vitamin K2).
- Carnitine racemase (gene caiD), which catalyses the reversible conversion of crotonobetaine to L-carnitine in Escherichia coli.
- Methylmalonyl CoA decarboxylase (MMCD; EC 184.108.40.206), which has a hexameric structure (dimer of trimers).
- Carboxymethylproline synthase (CarB), which is involved in carbapenem biosynthesis.
- 6-oxo camphor hydrolase, which catalyses the desymmetrization of bicyclic beta-diketones to optically active keto acids.
- The alpha subunit of fatty acid oxidation complex, a multi-enzyme complex that catalyses the last three reactions in the fatty acid beta-oxidation cycle.
- AUH protein, a bifunctional RNA-binding homologue of enoyl-CoA hydratase.
Human proteins containing this domain
- Gerlt JA, Benning MM, Holden HM, Haller T (2001). "The crotonase superfamily: divergently related enzymes that catalyze different reactions involving acyl coenzyme a thioesters". Acc. Chem. Res. 34 (2): 145–57. doi:10.1021/ar000053l. PMID 11263873.
- Brzozowski AM, Leonard PM, Bennett JP, Whittingham JL, Grogan G (2007). "Structural characterization of a beta-diketone hydrolase from the cyanobacterium Anabaena sp. PCC 7120 in native and product-bound forms, a coenzyme A-independent member of the crotonase suprafamily". Biochemistry 46 (1): 137–44. doi:10.1021/bi061900g. PMID 17198383.
- Wu J, Kisker C, Whitty A, Feng Y, Rudolph MJ, Bell AF, Hofstein HA, Parikh S, Tonge PJ (2002). "Stereoselectivity of enoyl-CoA hydratase results from preferential activation of one of two bound substrate conformers". Chem. Biol. 9 (11): 1247–55. doi:10.1016/S1074-5521(02)00263-6. PMID 12445775.
- Stoffel W, Muller-Newen G (1991). "Mitochondrial 3-2trans-Enoyl-CoA isomerase. Purification, cloning, expression, and mitochondrial import of the key enzyme of unsaturated fatty acid beta-oxidation". Biol. Chem. Hoppe-Seyler 372 (8): 613–624. doi:10.1515/bchm3.1991.372.2.613. PMID 1958319.
- Dunaway-Mariano D, Benning MM, Wesenberg G, Holden HM, Taylor KL, Yang G, Liu R-Q, Xiang H (1996). "Structure of 4-chlorobenzoyl coenzyme A dehalogenase determined to 1.8 A resolution: an enzyme catalyst generated via adaptive mutation". Biochemistry 35 (25): 8103–9. doi:10.1021/bi960768p. PMID 8679561.
- Hiltunen JK, Wierenga RK, Modis Y, Filppula SA, Novikov DK, Norledge B (1998). "The crystal structure of dienoyl-CoA isomerase at 1.5 A resolution reveals the importance of aspartate and glutamate sidechains for catalysis". Structure 6 (8): 957–70. doi:10.1016/s0969-2126(98)00098-7. PMID 9739087.
- Baker EN, Johnston JM, Arcus VL (2005). "Structure of naphthoate synthase (MenB) from Mycobacterium tuberculosis in both native and product-bound forms". Acta Crystallogr. D 61 (Pt 9): 1199–206. doi:10.1107/S0907444905017531. PMID 16131752.
- Kleber HP, Elssner T, Engemann C, Baumgart K (2001). "Involvement of coenzyme A esters and two new enzymes, an enoyl-CoA hydratase and a CoA-transferase, in the hydration of crotonobetaine to L-carnitine by Escherichia coli". Biochemistry 40 (37): 11140–8. doi:10.1021/bi0108812. PMID 11551212.
- Gerlt JA, Benning MM, Holden HM, Haller T (2000). "New reactions in the crotonase superfamily: structure of methylmalonyl CoA decarboxylase from Escherichia coli". Biochemistry 39 (16): 4630–9. doi:10.1021/bi9928896. PMID 10769118.
- Schofield CJ, McDonough MA, Sleeman MC, Sorensen JL, Batchelar ET (2005). "Structural and mechanistic studies on carboxymethylproline synthase (CarB), a unique member of the crotonase superfamily catalyzing the first step in carbapenem biosynthesis". J. Biol. Chem. 280 (41): 34956–65. doi:10.1074/jbc.M507196200. PMID 16096274.
- Leonard PM, Grogan G (2004). "Structure of 6-oxo camphor hydrolase H122A mutant bound to its natural product, (2S,4S)-alpha-campholinic acid: mutant structure suggests an atypical mode of transition state binding for a crotonase homolog". J. Biol. Chem. 279 (30): 31312–17. doi:10.1074/jbc.M403514200. PMID 15138275.
- Resibois-Gregoire A, Dourov N (1966). "Electron microscopic study of a case of cerebral glycogenosis". Acta Neuropathol. 6 (1): 70–9. doi:10.1007/BF00691083. PMID 5229654.
- Nureki O, Fukai S, Yokoyama S, Muto Y, Kurimoto K (2001). "Crystal structure of human AUH protein, a single-stranded RNA binding homolog of enoyl-CoA hydratase". Structure 9 (12): 1253–63. doi:10.1016/S0969-2126(01)00686-4. PMID 11738050.
Enoyl-CoA hydratase/isomerase family Provide feedback
This family contains a diverse set of enzymes including: Enoyl-CoA hydratase (Q13011). Napthoate synthase (P27290). Carnitate racemase (P31551). 3-hydoxybutyryl-CoA dehydratase (P52046). Dodecanoyl-CoA delta-isomerase (P42126).
Internal database links
|Similarity to PfamA using HHSearch:||Peptidase_S49|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR001753
The crotonase superfamily is comprised of mechanistically diverse proteins that share a conserved trimeric quaternary structure (sometimes a hexamer consisting of a dimer of trimers), the core of which consists of 4 turns of a (beta/beta/alpha)n superhelix. Some enzymes in the superfamily have been shown to display dehalogenase, hydratase, and isomerase activities, while others have been implicated in carbon-carbon bond formation and cleavage as well as the hydrolysis of thioesters [PUBMED:11263873]. However, these different enzymes share the need to stabilise an enolate anion intermediate derived from an acyl-CoA substrate. This is accomplished by two structurally conserved peptidic NH groups that provide hydrogen bonds to the carbonyl moieties of the acyl-CoA substrates and form an "oxyanion hole". The CoA thioester derivatives bind in a characteristic hooked shape and a conserved tunnel binds the pantetheine group of CoA, which links the 3'-phosphate ADP binding site to the site of reaction [PUBMED:17198383]. Enzymes in the crotonase superfamily include:
- Enoyl-CoA hydratase (crotonase; EC), which catalyses the hydratation of 2-trans-enoyl-CoA into 3-hydroxyacyl-CoA [PUBMED:12445775].
- 3-2trans-enoyl-CoA isomerase (or dodecenoyl-CoA isomerise; EC), which shifts the 3-double bond of the intermediates of unsaturated fatty acid oxidation to the 2-trans position [PUBMED:1958319].
- 3-hydroxbutyryl-CoA dehydratase (crotonase; EC), a bacterial enzyme involved in the butyrate/butanol-producing pathway.
- 4-Chlorobenzoyl-CoA dehalogenase (EC), a Pseudomonas enzyme which catalyses the conversion of 4-chlorobenzoate-CoA to 4-hydroxybenzoate-CoA [PUBMED:8679561].
- Dienoyl-CoA isomerise, which catalyses the isomerisation of 3-trans,5-cis-dienoyl-CoA to 2-trans,4-trans-dienoyl-CoA [PUBMED:9739087].
- Naphthoate synthase (MenB, or DHNA synthetase; EC), a bacterial enzyme involved in the biosynthesis of menaquinone (vitamin K2) [PUBMED:16131752].
- Carnitine racemase (gene caiD), which catalyses the reversible conversion of crotonobetaine to L-carnitine in Escherichia coli [PUBMED:11551212].
- Methylmalonyl CoA decarboxylase (MMCD; EC), which has a hexameric structure (dimer of trimers) [PUBMED:10769118].
- Carboxymethylproline synthase (CarB), which is involved in carbapenem biosynthesis [PUBMED:16096274].
- 6-oxo camphor hydrolase, which catalyses the desymmetrisation of bicyclic beta-diketones to optically active keto acids [PUBMED:15138275].
- The alpha subunit of fatty oxidation complex, a multi-enzyme complex that catalyses the last three reactions in the fatty acid beta-oxidation cycle [PUBMED:5229654].
- AUH protein, a bifunctional RNA-binding homologue of enoyl-CoA hydratase [PUBMED:11738050].
This entry represents the core domain found in crotonase superfamily members.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||catalytic activity (GO:0003824)|
|Biological process||metabolic process (GO:0008152)|
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
Loading domain graphics...
This family includes several peptidases of peptidase clan SK as well as crotonase like proteins.
The clan contains the following 10 members:ACCA Carboxyl_trans CLP_protease ECH ECH_C MdcE Peptidase_S41 Peptidase_S49 Peptidase_S49_N SDH_sah
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- Pfam viewer
- an HTML-based viewer that uses DAS to retrieve alignment fragments on request
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
If you find these logos useful in your own work, please consider citing the following article:
Note: You can also download the data file for the tree.
Curation and family details
|Number in seed:||13|
|Number in full:||26211|
|Average length of the domain:||233.90 aa|
|Average identity of full alignment:||23 %|
|Average coverage of the sequence by the domain:||67.75 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||15|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
- 0 sequences
- 0 species
How the sunburst is generated
Colouring and labels
Anomalies in the taxonomy tree
Missing taxonomic levels
Unmapped species names
Too many species/sequences
The tree shows the occurrence of this domain across different species. More...
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
There are 2 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 ECH domain has been found. There are 502 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 seqence.
Loading structure mapping...