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38  structures 8295  species 0  interactions 23664  sequences 166  architectures

Family: Aconitase_C (PF00694)

Summary: Aconitase C-terminal domain

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Aconitase C-terminal domain Provide feedback

Members of this family usually also match to PF00330. This domain undergoes conformational change in the enzyme mechanism [1].

Literature references

  1. Lauble H, Stout CD; , Proteins 1995;22:1-11.: Steric and conformational features of the aconitase mechanism. PUBMED:7675781 EPMC:7675781

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000573

This entry represents the 'swivel' domain found at the C-terminal of eukaryotic mAcn, cAcn/IPR1 and IRP2, and bacterial AcnA. This domain has a three layer beta/beta/alpha structure, and in cytosolic Acn is known to rotate between the cAcn and IRP1 forms of the enzyme. This domain is also found in the small subunit of isopropylmalate dehydratase (LeuD).

Aconitase (aconitate hydratase; EC ) is an iron-sulphur protein that contains a [4Fe-4S]-cluster and catalyses the interconversion of isocitrate and citrate via a cis-aconitate intermediate. Aconitase functions in both the TCA and glyoxylate cycles, however unlike the majority of iron-sulphur proteins that function as electron carriers, the [4Fe-4S]-cluster of aconitase reacts directly with an enzyme substrate. In eukaryotes there is a cytosolic form (cAcn) and a mitochondrial form (mAcn) of the enzyme. In bacteria there are also 2 forms, aconitase A (AcnA) and B (AcnB). Several aconitases are known to be multi-functional enzymes with a second non-catalytic, but essential function that arises when the cellular environment changes, such as when iron levels drop [ PUBMED:10087914 , PUBMED:15877277 ]. Eukaryotic cAcn and mAcn, and bacterial AcnA have the same domain organisation, consisting of three N-terminal alpha/beta/alpha domains, a linker region, followed by a C-terminal 'swivel' domain with a beta/beta/alpha structure (1-2-3-linker-4), although mAcn is small than cAcn. However, bacterial AcnB has a different organisation: it contains an N-terminal HEAT-like domain, followed by the 'swivel' domain, then the three alpha/beta/alpha domains (HEAT-4-1-2-3) [ PUBMED:9020582 ].

3-isopropylmalate dehydratase (or isopropylmalate isomerase; IPMI; EC ) catalyses the stereo-specific isomerisation of 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. This enzyme performs the second step in the biosynthesis of leucine, and is present in most prokaryotes and many fungal species. The prokaryotic enzyme is a heterodimer composed of a large (LeuC) and small (LeuD) subunit, while the fungal form is a monomeric enzyme. Both forms of isopropylmalate are related and are part of the larger aconitase family [ PUBMED:9020582 ].

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 Leu-IlvD (CL0364), which has the following description:

Superfamily includes LeuD-like, IlvD/EDD C-terminal domain-like, and AF0055-like families.

The clan contains the following 10 members:

AcnX_swivel_put Aconitase_2_N Aconitase_C CPSase_sm_chain Cyclase DUF2172 PA PEP-utilizers Peptidase_S66C RraA-like


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.

Representative proteomes UniProt
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Representative proteomes UniProt

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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.

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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...


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: Pfam-B_224 (release 2.1)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 11
Number in full: 23664
Average length of the domain: 120.90 aa
Average identity of full alignment: 32 %
Average coverage of the sequence by the domain: 20.46 %

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 22.8 22.8
Trusted cut-off 22.8 22.8
Noise cut-off 22.7 22.7
Model length: 131
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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Colour assignments

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


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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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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 Aconitase_C domain has been found. There are 38 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
A0A096UAZ3 View 3D Structure Click here
A0A0N7KLZ5 View 3D Structure Click here
A0A1D6EGA7 View 3D Structure Click here
A0A1D6EWX1 View 3D Structure Click here
A0A1D6H2F2 View 3D Structure Click here
A0A1D6J2H2 View 3D Structure Click here
A0A1D6J321 View 3D Structure Click here
A0A1D6JN03 View 3D Structure Click here
A0A1D6PJL0 View 3D Structure Click here
A0A1D6PUK8 View 3D Structure Click here
A0A1D8PRP8 View 3D Structure Click here
A0A1D8PT27 View 3D Structure Click here
A0A2R8RID5 View 3D Structure Click here
A0JMA0 View 3D Structure Click here
A0JXX7 View 3D Structure Click here
A0KGM6 View 3D Structure Click here
A0L8J5 View 3D Structure Click here
A0LVA2 View 3D Structure Click here
A0QX20 View 3D Structure Click here
A0ZZS8 View 3D Structure Click here
A1AW35 View 3D Structure Click here
A1B515 View 3D Structure Click here
A1K4A2 View 3D Structure Click here
A1R7J9 View 3D Structure Click here
A1S2E3 View 3D Structure Click here
A1SLW4 View 3D Structure Click here
A1SVE8 View 3D Structure Click here
A1T701 View 3D Structure Click here
A1TLH5 View 3D Structure Click here
A1UEA9 View 3D Structure Click here
A1VRR1 View 3D Structure Click here
A1WAT0 View 3D Structure Click here
A2SHT0 View 3D Structure Click here
A3CMJ3 View 3D Structure Click here
A3MYL0 View 3D Structure Click here
A3QIN7 View 3D Structure Click here
A4FMP1 View 3D Structure Click here
A4HXS6 View 3D Structure Click here
A4VKE8 View 3D Structure Click here
A4VXS3 View 3D Structure Click here