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941  structures 7393  species 0  interactions 76081  sequences 504  architectures

Family: ECH_1 (PF00378)

Summary: Enoyl-CoA hydratase/isomerase

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 "Crotonase family". More...

Crotonase family Edit Wikipedia article

Enoyl-CoA hydratase/isomerase family
Identifiers
Symbol ECH
Pfam PF00378
InterPro IPR001753
PROSITE PDOC00150
SCOP 1dub
SUPERFAMILY 1dub
CDD cd06558

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.[1] 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.[2] Enzymes in the crotonase superfamily include:

Human proteins containing this domain

AUH; CDY2B; CDYL; CDYL2; DCI; ECH1; ECHDC1; ECHDC2; ECHDC3; ECHS1; EHHADH; HADHA; HCA64; HIBCH; PECI;

References

  1. ^ 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. 
  2. ^ 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. 
  3. ^ 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. 
  4. ^ 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. 
  5. ^ 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. 
  6. ^ 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. 
  7. ^ 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. 
  8. ^ 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. 
  9. ^ 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. 
  10. ^ 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. 
  11. ^ 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. 
  12. ^ 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. 
  13. ^ 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. 

This article incorporates text from the public domain Pfam and InterPro IPR001753

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.

Enoyl-CoA hydratase/isomerase Provide feedback

This family contains a diverse set of enzymes including: enoyl-CoA hydratase, napthoate synthase, carnitate racemase, 3-hydroxybutyryl-CoA dehydratase and dodecanoyl-CoA delta-isomerase.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001753

This family contains a diverse set of enzymes including: enoyl-CoA hydratase, 1,4-dihydroxy-2-naphthoyl-CoA synthase (napthoate synthase), carnitinyl-CoA dehydratase (carnitine racemase), 3-hydroxybutyryl-CoA dehydratase and enoyl-CoA delta isomerase (dodecanoyl-CoA delta-isomerase).

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 ClpP_crotonase (CL0127), which has the following description:

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_1 ECH_2 MdcE Peptidase_S41 Peptidase_S49 Peptidase_S49_N SDH_sah

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...

View options

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
(9)
Full
(76081)
Representative proteomes UniProt
(313934)
RP15
(8476)
RP35
(31449)
RP55
(73801)
RP75
(129776)
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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
(9)
Full
(76081)
Representative proteomes UniProt
(313934)
RP15
(8476)
RP35
(31449)
RP55
(73801)
RP75
(129776)
Alignment:
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Order:
Sequence:
Gaps:
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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
(9)
Full
(76081)
Representative proteomes UniProt
(313934)
RP15
(8476)
RP35
(31449)
RP55
(73801)
RP75
(129776)
Raw Stockholm Download   Download   Download   Download   Download      
Gzipped 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: Prosite
Previous IDs: ECH;
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD , Eberhardt R
Number in seed: 9
Number in full: 76081
Average length of the domain: 231.00 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 68.38 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.9 26.9
Model length: 251
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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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 ECH_1 domain has been found. There are 941 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
A0A0P0Y1F7 View 3D Structure Click here
A0A0R0EJZ5 View 3D Structure Click here
A0A0R0EL70 View 3D Structure Click here
A0A0R0F719 View 3D Structure Click here
A0A0R0JBY6 View 3D Structure Click here
A0A0R4IAH3 View 3D Structure Click here
A0A1D6FGJ6 View 3D Structure Click here
A0A1D6GE30 View 3D Structure Click here
A0A1D6H4X3 View 3D Structure Click here
A0A1D6HEY4 View 3D Structure Click here
A0A1D6HEY4 View 3D Structure Click here
A0A1D6HEY7 View 3D Structure Click here
A0A1D6M201 View 3D Structure Click here
A0A1D6MGA1 View 3D Structure Click here
A0A1D6MKX5 View 3D Structure Click here
A0A1D6QNT6 View 3D Structure Click here
A0A2R8QGS9 View 3D Structure Click here
A0A368UJF6 View 3D Structure Click here
A0PJR5 View 3D Structure Click here
A1Z934 View 3D Structure Click here
A3CAF5 View 3D Structure Click here
A4HXT3 View 3D Structure Click here
A4I289 View 3D Structure Click here
A4I438 View 3D Structure Click here
A4I4U5 View 3D Structure Click here
A4I708 View 3D Structure Click here
A4I738 View 3D Structure Click here
A7YT47 View 3D Structure Click here
B4FD65 View 3D Structure Click here
B6TPA4 View 3D Structure Click here
B7F9R1 View 3D Structure Click here
B7FAJ1 View 3D Structure Click here
C0HEB1 View 3D Structure Click here
C0P8K0 View 3D Structure Click here
C0PL35 View 3D Structure Click here
C6TE57 View 3D Structure Click here
C6TH01 View 3D Structure Click here
D1MN80 View 3D Structure Click here
D3ZIL6 View 3D Structure Click here
E7F6P0 View 3D Structure Click here
E9AHU0 View 3D Structure Click here
F1LT42 View 3D Structure Click here
F1LU71 View 3D Structure Click here
F1QYX8 View 3D Structure Click here
F1R2G5 View 3D Structure Click here
F1R6N4 View 3D Structure Click here
F1RDX1 View 3D Structure Click here
F4JML5 View 3D Structure Click here
I1K0U5 View 3D Structure Click here
I1KIP9 View 3D Structure Click here
I1L4J2 View 3D Structure Click here
I1L7J3 View 3D Structure Click here
I1M292 View 3D Structure Click here
I1MRJ8 View 3D Structure Click here
I1MRK1 View 3D Structure Click here
I1MV56 View 3D Structure Click here
I1N551 View 3D Structure Click here
I6Y3U6 View 3D Structure Click here
I6Y4E8 View 3D Structure Click here
I6Y8B5 View 3D Structure Click here
I6Y8F2 View 3D Structure Click here
I6Y8F2 View 3D Structure Click here
I6YA03 View 3D Structure Click here
I6YEH6 View 3D Structure Click here
K7MS06 View 3D Structure Click here
O04469 View 3D Structure Click here
O06536 View 3D Structure Click here
O06541 View 3D Structure Click here
O06542 View 3D Structure Click here
O07179 View 3D Structure Click here
O17612 View 3D Structure Click here
O23299 View 3D Structure Click here
O23300 View 3D Structure Click here
O35459 View 3D Structure Click here
O45106 View 3D Structure Click here
O50402 View 3D Structure Click here
O53561 View 3D Structure Click here
O53872 View 3D Structure Click here
O75521 View 3D Structure Click here
P07896 View 3D Structure Click here
P0ABU0 View 3D Structure Click here
P14604 View 3D Structure Click here
P21177 View 3D Structure Click here
P23965 View 3D Structure Click here
P30084 View 3D Structure Click here
P31551 View 3D Structure Click here
P34559 View 3D Structure Click here
P40939 View 3D Structure Click here
P41942 View 3D Structure Click here
P42125 View 3D Structure Click here
P42126 View 3D Structure Click here
P52045 View 3D Structure Click here
P71540 View 3D Structure Click here
P75019 View 3D Structure Click here
P76082 View 3D Structure Click here
P77399 View 3D Structure Click here
P77467 View 3D Structure Click here
P91130 View 3D Structure Click here
P95279 View 3D Structure Click here
P95279 View 3D Structure Click here
P96404 View 3D Structure Click here
P9WNN3 View 3D Structure Click here
P9WNN5 View 3D Structure Click here
P9WNN7 View 3D Structure Click here
P9WNN9 View 3D Structure Click here
P9WNP1 View 3D Structure Click here
P9WNP5 View 3D Structure Click here
Q05871 View 3D Structure Click here
Q08426 View 3D Structure Click here
Q08558 View 3D Structure Click here
Q09603 View 3D Structure Click here
Q0DKM2 View 3D Structure Click here
Q10MF8 View 3D Structure Click here
Q13011 View 3D Structure Click here
Q13825 View 3D Structure Click here
Q1ZXF1 View 3D Structure Click here
Q20376 View 3D Structure Click here
Q20959 View 3D Structure Click here
Q2FZL5 View 3D Structure Click here
Q2G1C9 View 3D Structure Click here
Q3MIE0 View 3D Structure Click here
Q3TLP5 View 3D Structure Click here
Q4CKX1 View 3D Structure Click here
Q4CL61 View 3D Structure Click here
Q4CLW3 View 3D Structure Click here
Q4CRI1 View 3D Structure Click here
Q4CTQ3 View 3D Structure Click here
Q4CWB6 View 3D Structure Click here
Q4CWM5 View 3D Structure Click here
Q4CXJ3 View 3D Structure Click here
Q4D8W2 View 3D Structure Click here
Q4DB76 View 3D Structure Click here
Q4DIE0 View 3D Structure Click here
Q4E5H2 View 3D Structure Click here
Q4E679 View 3D Structure Click here
Q54BX7 View 3D Structure Click here
Q54HG7 View 3D Structure Click here
Q54HX9 View 3D Structure Click here
Q54SN3 View 3D Structure Click here
Q54SS0 View 3D Structure Click here
Q5A318 View 3D Structure Click here
Q5A320 View 3D Structure Click here
Q5ADL1 View 3D Structure Click here
Q5TYQ4 View 3D Structure Click here
Q5XIC0 View 3D Structure Click here
Q60E84 View 3D Structure Click here
Q62651 View 3D Structure Click here
Q64428 View 3D Structure Click here
Q65XC3 View 3D Structure Click here
Q6AYG5 View 3D Structure Click here
Q6AYK9 View 3D Structure Click here
Q6H7I3 View 3D Structure Click here
Q6NL24 View 3D Structure Click here
Q6NYL3 View 3D Structure Click here
Q75JJ9 View 3D Structure Click here
Q78JN3 View 3D Structure Click here
Q7JR58 View 3D Structure Click here
Q7K1C3 View 3D Structure Click here
Q7ZZ04 View 3D Structure Click here
Q869N6 View 3D Structure Click here
Q86YB7 View 3D Structure Click here
Q8BH95 View 3D Structure Click here
Q8BMS1 View 3D Structure Click here
Q8GYN9 View 3D Structure Click here
Q8ILL1 View 3D Structure Click here
Q8LR33 View 3D Structure Click here
Q8N8U2 View 3D Structure Click here
Q8RUL6 View 3D Structure Click here
Q8W1L6 View 3D Structure Click here
Q94CN1 View 3D Structure Click here
Q96DC8 View 3D Structure Click here
Q9D5D8 View 3D Structure Click here
Q9D7J9 View 3D Structure Click here
Q9D9V3 View 3D Structure Click here
Q9DBM2 View 3D Structure Click here
Q9FHR8 View 3D Structure Click here
Q9GYT0 View 3D Structure Click here
Q9JLZ3 View 3D Structure Click here
Q9LEA0 View 3D Structure Click here
Q9NEZ8 View 3D Structure Click here
Q9NTX5 View 3D Structure Click here
Q9TYL2 View 3D Structure Click here
Q9V397 View 3D Structure Click here
Q9VB17 View 3D Structure Click here
Q9VG69 View 3D Structure Click here
Q9VL66 View 3D Structure Click here
Q9VL67 View 3D Structure Click here
Q9VL68 View 3D Structure Click here
Q9VPB0 View 3D Structure Click here
Q9W0M0 View 3D Structure Click here
Q9W5W8 View 3D Structure Click here
Q9WTK2 View 3D Structure Click here
Q9WUR2 View 3D Structure Click here
Q9Y232 View 3D Structure Click here
Q9Y6F7 View 3D Structure Click here
Q9Y6F8 View 3D Structure Click here
Q9ZPI5 View 3D Structure Click here
Q9ZPI6 View 3D Structure Click here