Carbonic anhydrase
What InterPro tells us
Below are examples from InterPro for each of the three classes of carbonic anhydrase enzymes, and their family relationships with other proteins.
P00915 Human carbonic anhydrase I (alpha-class)
entry from InterPro
|
Interpro Entry |
Method accession |
Graphical match |
Method name |
|
IPR001148 |
PD000865 |
|
Euk_COanhd |
|
IPR001148 |
PF00194 |
|
carb_anhydrase |
|
IPR001148 |
PS00162 |
|
EUK_CO2_ANHYDRASE |
|
IPR001148 |
SSF51069 |
|
Euk_COanhd |
|
NONE |
1j9wA0 |
|
1j9wA0 |
|
NONE |
d1azm__ |
|
d1azm__ |
From the graphical match above, you can see that the signatures in InterPro for the human alpha-class carbonic anhydrase I protein fall into a single entry, IPR001148, which represents the eukaryotic carbonic anhydrase family. The four signatures in this entry are: PD000865 from the PRODOM database, PF00194 from the PFAM database, SSF51069 from the SUPERFAMILY database, and PS00162 from the PROSITE database, the latter being derived from one of the three conserved zinc-binding histidines. The remaining two entries in the table are from the structural classification databases CATH (1j9wA0) and SCOP (d1azm__); the names such as d1azm__ are derived from the PDB entry upon which they are based, here PDB entry 1azm. If you follow the links to these databases you will find descriptions of the structural features and classification of these domains, as well as links to the corresponding PDB entries; for instance, SCOP classifies the alpha-class carbonic anhydrase family as being within the carbonic anhydrase superfamily, containing a carbonic anhydrase fold.
P17067 Garden Pea carbonic anhydrase (beta-class)
entry from InterPro
|
Interpro Entry |
Method accession |
Graphical match |
Method name |
|
IPR001765 |
PF00484 |
|
Pro_CA |
|
IPR001765 |
PS00704 |
|
PROK_CO2_ANHYDRASE_1 |
|
IPR001765 |
PS00705 |
|
PROK_CO2_ANHYDRASE_2 |
|
IPR001765 |
SSF53056 |
|
Prok_COanhd |
|
NONE |
1ekjA0 |
|
1ekjA0 |
|
NONE |
d1ekja_ |
|
d1ekja_ |
From the second graphical match, you can see that the signatures in InterPro for the garden pea beta-class carbonic anhydrase protein fall into a single entry, IPR001765, which represents the prokaryotic and plant carbonic anhydrase domain. This entry is considered to be a domain rather than a family, as some proteins, such as the carbonic anhydrase of the red algae Porphyridium purpeum, can exist as two duplicated copies of this domain. The four signatures in this entry are: PF00484 from the PFAM database, SSF53056 from the SUPERFAMILY database, and PS00704 and PS00705 from the PROSITE database, the latter two being derived from conserved residues that could be involved in binding zinc (cysteine and histidine). The remaining two entries in the table are from the structural classification databases CATH (1ekjA0) and SCOP (d1ekja_), which supply descriptions of the structural features and classification of these domains, and links to the corresponding PDB entries. For instance, SCOP classifies the beta-class carbonic anhydrase family as being within the beta-carbonic anhydrase superfamily, containing a resolvase-like fold.
P40881 Archaeon carbonic anhydrase (gamma-class)
entry from InterPro
|
Interpro Entry |
Method accession |
Graphical match |
Method name |
|
IPR000437 |
PS00013 |
|
PROKAR_LIPOPROTEIN |
|
IPR001451 |
PF00132 |
|
hexapep |
|
NONE |
1qq0A0 |
|
1qq0A0 |
|
NONE |
d1qq0a_ |
|
d1qq0a_ |
From the third graphical match,
you can see that the signatures in InterPro for the archaeon gamma-class
carbonic anhydrase protein fall into two entries, IPR000437,
which represents the prokaryotic membrane lipoprotein attachment site, and IPR001451,
which represents the bacterial transferase hexapeptide repeat. The IPR000437 PS00013 signature from the
PROSITE database recognises those members of the gamma-class carbonic
anhydrases that are membrane-bound, this signature being derived from a
consensus pattern within the precursor signal peptide sequences. The IPR001451 PF00132 signature from the PFAM
database represents a tandem hexapeptide repeat found in a variety of bacterial
transferases, including LpxA, in addition to the gamma-class carbonic
anhydrases. The remaining two entries in
the table are from the structural classification databases CATH (1qq0A0) and SCOP (d1qq0a_), which supply descriptions of the structural features and classification
of these domains, and links to the corresponding PDB entries. For instance, SCOP classifies the
gamma-class carbonic anhydrase family as being within the trimeric LpxA-like
enzymes superfamily, containing a single-stranded left-handed beta helix fold.
Structural features of carbonic anhydrase
The crystallographic structures of several carbonic anhydrases from all three classes have been determined. A description and visualisation of the structural features of carbonic anhydrases can be found at the PDB database. Here you can see the structural basis for the carbonic anhydrase mechanism of action.