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51  structures 7069  species 0  interactions 21402  sequences 123  architectures

Family: E3_binding (PF02817)

Summary: e3 binding domain

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e3 binding domain Provide feedback

This family represents a small domain of the E2 subunit of 2-oxo-acid dehydrogenases responsible for the binding of the E3 subunit.

Literature references

  1. Mande SS, Sarfaty S, Allen MD, Perham RN, Hol WG; , Structure 1996;4:277-286.: Protein-protein interactions in the pyruvate dehydrogenase multienzyme complex: dihydrolipoamide dehydrogenase complexed with the binding domain of dihydrolipoamide acetyltransferase. PUBMED:8805537 EPMC:8805537


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004167

The ubiquitous 2-oxoacid dehydrogenases are a family of very large multienzyme complexes consisting of multiple copies of at least three enzymes which catalyze the oxidative decarboxylation of several different 2-oxoacids, resulting in acyl-CoA products. Members of this family include pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2- oxoacid dehydrogenase (BCDH). The three enzymes assembling to form these complexes are the decarboxylase E1 (called E1p, E1o and E1b in PDH, OGDH and BCDH, respectively), dihydrolipoamide acetyl, succinyl and branched-chain transferase E2 (E2p, E2o and E2b, respectively) and dihydrolipoamide dehydrogenase E3. The E3 component is identical in all three complexes (PDH, OGDH and BCDH) and catalyzes the same reaction. The structural core of all 2- oxoacid dehydrogenase complexes (ODHc) is formed of multiple copies of E2 subunits, with the E1 and E3 subunits bound on the periphery. The E2 component of the ODHc's of both bacteria and eukaryotes serves as the structural core of these multienzyme complexes and is comprised of three types of domains. Starting with the N terminus, there are 1-3 tandem repeated lipoyl domains (LD), followed by a peripheral subunit-binding domain (PSBD) responsible for binding E1/E3 chains. The third domain is the C-terminal catalytic domain (CD). The individual domains are separated by long, flexible linker regions allowing large movements of the lipoyl domain(s) to enable active site coupling. The PSBD domain binds E1 or E3, but not both simultaneously. The flexible linker allows the PSBD domain (associated with either E1 or E3) to move quite freely with respect to the core formed E2 catalytic domains [ PUBMED:1554728 , PUBMED:8805537 , PUBMED:10966480 , PUBMED:16442803 , PUBMED:24077172 ].

The ~35-residue PSBD domain has a compact structure consisting of two short, parallel alpha-helices (H1 and H2) separated by a loop (L1), a single helical turn, and a further, less well-ordered loop (L2) (see PDB:1BAL). The compact structure of the PSBD domain is stabilized mainly by hydrophobic interactions. The interactions between the PSBD domain and E3 are all mediated by charged side chains, forming an 'electrostatic zipper'. The residues of the PSBD domain involved in the interactions are all provided by helix H1 of this domain. Helix H2 of PSBD does not interact with E3, but may be involved in binding E1 [ PUBMED:1554728 , PUBMED:8805537 , PUBMED:16442803 ].

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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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
(811)
Full
(21402)
Representative proteomes UniProt
(86018)
RP15
(2677)
RP35
(9530)
RP55
(20801)
RP75
(34976)
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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
(811)
Full
(21402)
Representative proteomes UniProt
(86018)
RP15
(2677)
RP35
(9530)
RP55
(20801)
RP75
(34976)
Alignment:
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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
(811)
Full
(21402)
Representative proteomes UniProt
(86018)
RP15
(2677)
RP35
(9530)
RP55
(20801)
RP75
(34976)
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: Homstrad
Previous IDs: e3_binding;
Type: Family
Sequence Ontology: SO:0100021
Author: Griffiths-Jones SR
Number in seed: 811
Number in full: 21402
Average length of the domain: 35.80 aa
Average identity of full alignment: 40 %
Average coverage of the sequence by the domain: 7.80 %

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 23.7 23.7
Trusted cut-off 23.7 23.7
Noise cut-off 23.6 23.6
Model length: 36
Family (HMM) version: 19
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

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 E3_binding domain has been found. There are 51 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
A0A0R0EDH2 View 3D Structure Click here
A0A0R0I683 View 3D Structure Click here
A0A0R0JI69 View 3D Structure Click here
A0A0R0LFB4 View 3D Structure Click here
A0A1D6H6Z1 View 3D Structure Click here
A0A1D6I451 View 3D Structure Click here
A0A1D6KPB2 View 3D Structure Click here
A0A1D6L8E8 View 3D Structure Click here
A0A1D6MYM9 View 3D Structure Click here
A0A1D6Q1G1 View 3D Structure Click here
A0A1D6QQD9 View 3D Structure Click here
A0A2R8Q4A3 View 3D Structure Click here
A4ICH2 View 3D Structure Click here
B2GV15 View 3D Structure Click here
B3DIV6 View 3D Structure Click here
B4G1C9 View 3D Structure Click here
B6TJY4 View 3D Structure Click here
E9AG63 View 3D Structure Click here
F1R0J8 View 3D Structure Click here
I1KH71 View 3D Structure Click here
I1LD65 View 3D Structure Click here
I1MJX0 View 3D Structure Click here
I1MRK4 View 3D Structure Click here
I1NFH4 View 3D Structure Click here
I1NHB5 View 3D Structure Click here
O00330 View 3D Structure Click here
O06159 View 3D Structure Click here
O59816 View 3D Structure Click here
O94709 View 3D Structure Click here
P06959 View 3D Structure Click here
P08461 View 3D Structure Click here
P0AFG6 View 3D Structure Click here
P10515 View 3D Structure Click here
P11182 View 3D Structure Click here
P12695 View 3D Structure Click here
P16451 View 3D Structure Click here
P36413 View 3D Structure Click here
P53395 View 3D Structure Click here
P9WIS7 View 3D Structure Click here
Q0WQF7 View 3D Structure Click here
Q19749 View 3D Structure Click here
Q23571 View 3D Structure Click here
Q2FY54 View 3D Structure Click here
Q2FYM2 View 3D Structure Click here
Q2G2A4 View 3D Structure Click here
Q2QWU7 View 3D Structure Click here
Q4D8Z1 View 3D Structure Click here
Q4DDM3 View 3D Structure Click here
Q4DMG9 View 3D Structure Click here
Q4DZT8 View 3D Structure Click here
Q54TR7 View 3D Structure Click here
Q5AGX8 View 3D Structure Click here
Q5AKV6 View 3D Structure Click here
Q5M729 View 3D Structure Click here
Q5VS74 View 3D Structure Click here
Q654L9 View 3D Structure Click here
Q655Q2 View 3D Structure Click here
Q69N33 View 3D Structure Click here
Q6YPG2 View 3D Structure Click here
Q6ZKB1 View 3D Structure Click here
Q7TQ85 View 3D Structure Click here
Q7XAL3 View 3D Structure Click here
Q86AD5 View 3D Structure Click here
Q8BKZ9 View 3D Structure Click here
Q8BMF4 View 3D Structure Click here
Q8RWN9 View 3D Structure Click here
Q9C8P0 View 3D Structure Click here
Q9M7Z1 View 3D Structure Click here
Q9SQI8 View 3D Structure Click here
Q9VXY3 View 3D Structure Click here