Aconitase
What InterPro Tells Us
P21399 Human Iron Regulatory Protein 1 (cytosolic aconitase)
InterPro Domain Architecture
InterPro Entry |
Signatures |
Graphical Match |
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IPR012084 |
PIRSF001417 |
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TIGR01341 |
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IPR001030 |
PD000511 |
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IPR001030 |
PF00330 |
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IPR001030 |
PR00415 |
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IPR001030 |
PS00450 |
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IPR001030 |
PS01244 |
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IPR001030 |
SSF53732 |
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IPR000573 |
PF00694 |
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Structural Features |
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PDB |
2b3y (A,B) |
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From the graphical match in the table above, you can see that the signatures are grouped into four InterPro entries for human IRP1/cAcn. InterPro entries group together all the signatures that represent the same sequence found in the same set of proteins. These entries provide a family hierarchy of IRP1 proteins, as well as identifying the domain architecture and sequence features of this protein.
FAMILY Entries
Ø IPR012084: Aconitase/homoaconitase, represented by one signature: PIRSF001417 (PIRSF).
Ø IPR006249: Aconitate hydratase 1, represented by one signature: TIGR01341 (TIGRFAMs).
The two family groupings are hierarchical, covering the same sequence in expanding sets of proteins. The first entry, IPR012084, is top of the hierarchy representing the aconitase/homoaconitase family of proteins. As such, its signature hits the largest group of proteins. This entry has two ‘child’ entries that cover the same sequence, but in different non-overlapping sets of proteins. These children are all shown in the tree below; the one that relates to the above protein is IPR006249, the aconitate hydratase 1 subfamily (the other subfamily, IPR012708, represents 2-methylisocitrate dehydrogenase, which is homologous to aconitase).
DOMAIN Entries
Ø IPR001030: Iron-sulphur domain of aconitate hydratase, represented by six signatures: PD000511 (ProDom), PF00330 (PFAM), PR00415 (PRINTS), PS00450 and PS01244 (PROSITE), and SSF53732 (SUPERFAMILY).
Ø IPR000573: C-terminal domain of aconitate hydratase, represented by one signature: PF00694 (PFAM).
The graphical match shows that
human iron regulatory protein 1/aconitase can be subdivided into two
regions. The first region is covered by
IPR001030, and represents the iron-sulphur cluster binding region. This region is composed of three structurally
similar domains, each of which consists of three layers, alpha/beta/alpha. In aconitase 1 (or aconitase A) this domain
is found at the N-terminus, while in aconitase B it is found at the C-terminus. The two PROSITE signatures in IPR001030
identify the iron-sulphur cluster binding sites: PS00450 contains the first
conserved Cys and PS01244 contains
the second and third conserved Cys of the 4Fe-4S cluster.
The second region is covered by IPR000573, and represents the “swivelling” domain, which has a beta/beta/alpha structure. In aconitase A this domain is found at the C-terminus, while in aconitase B a structurally homologous domain is found as the second N-terminal domain.
Structural features
The remaining entry in the
table above gives information on the known structure of this protein, and is
from the structural database PDB (green stripe). The graphical match for the PDB entry 2b3y displays the full length of the original PDB entry, here
covering the entire protein. This PDB
has not yet been classified by either CATH or SCOP, so the structurally-defined
domain information is not yet available.
What the Structure Tells Us
There are structures available for
several iron regulatory proteins and/or aconitases from different organisms in the
Protein Data Bank (PDB). A detailed
description and visualisation of the structural features of the bi-functional
proteins can be found at the PDB ‘Molecule of the Month’.
The crystallographic structures of various bi-functional and
mono-functional iron regulatory protein/aconitases have provided insight into
their mechanism of action, as well as the molecular switch mechanism found in
the bi-functional proteins.