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51  structures 6852  species 5  interactions 18000  sequences 97  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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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
(969)
Full
(18000)
Representative proteomes UniProt
(48298)
NCBI
(71527)
Meta
(3900)
RP15
(4006)
RP35
(11205)
RP55
(17640)
RP75
(24905)
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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
(969)
Full
(18000)
Representative proteomes UniProt
(48298)
NCBI
(71527)
Meta
(3900)
RP15
(4006)
RP35
(11205)
RP55
(17640)
RP75
(24905)
Alignment:
Format:
Order:
Sequence:
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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
(969)
Full
(18000)
Representative proteomes UniProt
(48298)
NCBI
(71527)
Meta
(3900)
RP15
(4006)
RP35
(11205)
RP55
(17640)
RP75
(24905)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   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: 969
Number in full: 18000
Average length of the domain: 35.70 aa
Average identity of full alignment: 41 %
Average coverage of the sequence by the domain: 7.84 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.5 23.5
Trusted cut-off 23.5 23.5
Noise cut-off 23.4 23.4
Model length: 36
Family (HMM) version: 17
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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Interactions

There are 5 interactions for this family. More...

Pyr_redox Pyr_redox_2 Pyr_redox_2 Pyr_redox_dim Transketolase_C

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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