Summary: Eukaryotic-type carbonic anhydrase

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Carbonic anhydrase Edit Wikipedia article

Carbonate dehydratase

Ribbon diagram of human carbonic anhydrase II, with zinc ion visible in the center

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Eukaryotic-type carbonic anhydrase

Identifiers

Symbol

Carb_anhydrase

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

The carbonic anhydrases (or carbonate dehydratases) form a family of enzymes that catalyze the rapid interconversion of carbon dioxide and water to bicarbonate and protons (or vice versa), a reversible reaction that occurs rather slowly in the absence of a catalyst.^[1] The active site of most carbonic anhydrases contains a zinc ion; they are therefore classified as metalloenzymes.

One of the functions of the enzyme in animals is to interconvert carbon dioxide and bicarbonate to maintain acid-base balance in blood and other tissues, and to help transport carbon dioxide out of tissues.

Reaction

The reaction catalyzed by carbonic anhydrase is:

$\rm CO_2 + H_2O \xrightarrow{Carbonic\ anhydrase} H_2CO_3$ (in tissues - high CO₂ concentration)^[2]

The reaction rate of carbonic anhydrase is one of the fastest of all enzymes, and its rate is typically limited by the diffusion rate of its substrates. Typical catalytic rates of the different forms of this enzyme ranging between 10⁴ and 10⁶ reactions per second.^[3]

The reverse reaction is relatively slow (kinetics in the 15-second range) in the absence of a catalyst. This is why a carbonated drink does not instantly degas when opening the container; however it will rapidly degas in the mouth when it comes in contact with carbonic anhydrase that is contained in saliva.^[4]

An anhydrase is defined as an enzyme that catalyzes the removal of a water molecule from a compound, and so it is this "reverse" reaction that gives carbonic anhydrase its name, because it removes a water molecule from carbonic acid.

$\rm HCO_3^- + H^+ \rightarrow H_2CO_3 \rightarrow CO_2 + H_2O$ (in lungs and nephrons of the kidney - low CO₂ concentration, in plant cells)

Mechanism

Close-up rendering of active site of human carbonic anhydrase II, showing three histidine residues and a hydroxide group coordinating (dashed lines) the zinc ion at center. From PDB 1CA2.

A zinc prosthetic group in the enzyme is coordinated in three positions by histidine side-chains. The fourth coordination position is occupied by water. This causes polarisation of the hydrogen-oxygen bond, making the oxygen slightly more negative, thereby weakening the bond.

A fourth histidine is placed close to the substrate of water and accepts a proton, in an example of general acid - general base catalysis (see the article "Acid catalysis"). This leaves a hydroxide attached to the zinc.

The active site also contains specificity pocket for carbon dioxide, bringing it close to the hydroxide group. This allows the electron-rich hydroxide to attack the carbon dioxide, forming bicarbonate.

CA families

Ribbon diagram of human carbonic anhydrase II. Active site zinc ion visible at center. From PDB 1CA2.

There are at least five distinct CA families (α, β, γ, δ and ε). These families have no significant amino acid sequence similarity and in most cases are thought to be an example of convergent evolution. The α-CAs are found in humans.

α-CA

The CA enzymes found in mammals are divided into four broad subgroups,^[5] which, in turn consist of several isoforms:

the cytosolic CAs (CA-I, CA-II, CA-III, CA-VII and CA XIII) (CA1, CA2, CA3, CA7, CA13)
mitochondrial CAs (CA-VA and CA-VB) (CA5A, CA5B)
secreted CAs (CA-VI) (CA6)
membrane-associated CAs (CA-IV, CA-IX, CA-XII, CA-XIV and CA-XV) (CA4, CA9, CA12, CA14)

There are three additional "acatalytic" CA isoforms (CA-VIII, CA-X, and CA-XI) (CA8, CA10, CA11) whose functions remain unclear.^[6]

Comparison of mammalian carbonic anhydrases
Isoform	Gene	Molecular mass^[7]	Location (cell)	Location (tissue)^[7]	Specific activity of human enzymes (except for mouse CA XV) (s⁻¹) ^[8]	Sensitivity to sulfonamides (acetazolamide in this table) K_I (nM) ^[8]
CA-I	CA1	29 kDa	cytosol	red blood cell and GI tract	2.0 × 10⁵	250
CA-II	CA2	29 kDa	cytosol	almost ubiquitous	1.4 × 10⁶	12
CA-III	CA3	29 kDa	cytosol	8% of soluble protein in Type I muscle	1.3 × 10⁴	240000
CA-IV	CA4	35 kDa	extracellular GPI-linked	GI tract, kidney, endothelium	1.1 × 10⁶	74
CA-VA	CA5A	34.7 kDa (predicted)	mitochondria	liver	2.9 × 10⁵	63
CA-VB	CA5B	36.4 kDa (predicted)	mitochondria	widely distributed	9.5 × 10⁵	54
CA-VI	CA6	39-42 kDa	secretory	saliva and milk	3.4 × 10⁵	11
CA-VII	CA7	29 kDa	cytosol	widely distributed	9.5 × 10⁵	2.5
CA-IX	CA9	54, 58 kDa	cell membrane-associated	normal GI tract, several cancers	1.1 × 10⁶	16
CA-XII	CA12	44 kDa	extracellularily located active site	kidney, certain cancers	4.2 × 10⁵	5.7
CA-XIII ^[9]	CA13	29 kDa	cytosol	widely distributed	1.5 × 10⁵	16
CA-XIV	CA14	54 kDa	extracellularily located active site	kidney, heart, skeletal muscle, brain	3.1 × 10⁵	41
CA-XV ^[10]	CA15	34-36 kDa	extracellular GPI-linked	kidney, not expressed in human tissues	4.7 × 10⁵	72

β-CA

Most prokaryotic and plant chloroplast CAs belong to the beta family. Two signature patterns for this family have been identified:

C-[SA]-D-S-R-[LIVM]-x-[AP]
[EQ]-[YF]-A-[LIVM]-x(2)-[LIVM]-x(4)-[LIVMF](3)-x-G-H-x(2)-C-G

γ-CA

The gamma class of CAs come from methane-producing bacteria that grow in hot springs.

δ-CA

The delta class of CAs has been described in diatoms. The distinction of this class of CA has recently^[11] come into question, however.

ε-CA

The epsilon class of CAs occurs exclusively in bacteria in a few chemolithotrophs and marine cyanobacteria that contain cso-carboxysomes.^[12] Recent 3-dimensional analyses^[11] suggest that ε-CA bears some structural resemblance to β-CA, particularly near the metal ion site. Thus, the two forms may be distantly related, even though the underlying amino acid sequence has since diverged considerably.

Pharmacological agents affecting CA

See Carbonic anhydrase inhibitors

Structure and function of carbonic anhydrase

Several forms of carbonic anhydrase occur in nature. In the best-studied α-carbonic anhydrase form present in animals, the zinc ion is coordinated by the imidazole rings of 3 histidine residues, His94, His96, and His119.

The primary function of the enzyme in animals is to interconvert carbon dioxide and bicarbonate to maintain acid-base balance in blood and other tissues, and to help transport carbon dioxide out of tissues.

There exist at least 14 different isoforms in mammals. Plants contain a different form called β-carbonic anhydrase, which, from an evolutionary standpoint, is a distinct enzyme, but participates in the same reaction and also uses a zinc ion in its active site. In plants, carbonic anhydrase helps raise the concentration of CO₂ within the chloroplast in order to increase the carboxylation rate of the enzyme RuBisCO. This is the reaction that integrates CO₂ into organic carbon sugars during photosynthesis, and can use only the CO₂ form of carbon, not carbonic acid or bicarbonate.

A cadmium-containing carbonic anhydrase was found to be expressed in marine diatoms during zinc limitation.^[13] In the open ocean, zinc is often in such low concentrations that it can limit the growth of phytoplankton like diatoms; thus, a carbonic anhydrase using a different metal ion would be beneficial in these environments. Cadmium has in general been thought of as a very toxic heavy metal without biological function. This peculiar carbonic anhydrase form hosts the only known beneficial cadmium-dependent biological reaction.^[13]

References

^ Badger MR, Price GD (1994). "The role of carbonic anhydrase in photosynthesis". Annu. Rev. Plant Physiol. Plant Mol. Bio. 45: 369–392. doi:10.1146/annurev.pp.45.060194.002101.
^ Carbonic acid has a pK_a of around 6.36 (the exact value depends on the medium) so at pH 7 a small percentage of the bicarbonate is protonated. See carbonic acid for details concerning the equilibria HCO₃^- + H⁺ $\rightleftharpoons$ H₂CO₃ and H₂CO₃ $\rightleftharpoons$ CO₂ + H₂O
^ Lindskog S (1997). "Structure and mechanism of carbonic anhydrase". Pharmacol. Ther. 74 (1): 1–20. doi:10.1016/S0163-7258(96)00198-2. PMID 9336012.
^ Thatcher BJ, Doherty AE, Orvisky E, Martin BM, Henkin RI (September 1998). "Gustin from human parotid saliva is carbonic anhydrase VI". Biochem. Biophys. Res. Commun. 250 (3): 635–41. doi:10.1006/bbrc.1998.9356. PMID 9784398.
^ Breton S (2001). "The cellular physiology of carbonic anhydrases". JOP 2 (4 Suppl): 159–64. PMID 11875253.
^ Lovejoy DA, Hewett-Emmett D, Porter CA, Cepoi D, Sheffield A, Vale WW, Tashian RE (1998). "Evolutionarily conserved, "acatalytic" carbonic anhydrase-related protein XI contains a sequence motif present in the neuropeptide sauvagine: the human CA-RP XI gene (CA11) is embedded between the secretor gene cluster and the DBP gene at 19q13.3". Genomics 54 (3): 484–93. doi:10.1006/geno.1998.5585. PMID 9878252.
^ ^a ^b Unless else specified: Walter F., PhD. Boron (2005). Medical Physiology: A Cellular And Molecular Approaoch. Elsevier/Saunders. ISBN 1-4160-2328-3. Page 638
^ ^a ^b Hilvo M, Baranauskiene L, Salzano AM, Scaloni A, Matulis D, Innocenti A, Scozzafava A, Monti SM, Di Fiore A, De Simone G, Lindfors M, Jänis J, Valjakka J, Pastoreková S, Pastorek J, Kulomaa MS, Nordlund HR, Supuran CT, Parkkila S (2008). "Biochemical characterization of CA IX, one of the most active carbonic anhydrase isozymes". J. Biol. Chem. 283 (41): 27799–809. doi:10.1074/jbc.M800938200. PMID 18703501.
^ Lehtonen J, Shen B, Vihinen M, Casini A, Scozzafava A, Supuran CT, Parkkila AK, Saarnio J, Kivelä AJ, Waheed A, Sly WS, Parkkila S (2004). "Characterization of CA XIII, a novel member of the carbonic anhydrase isozyme family". J. Biol. Chem. 279 (4): 2719–27. doi:10.1074/jbc.M308984200. PMID 14600151.
^ Hilvo M, Tolvanen M, Clark A, Shen B, Shah GN, Waheed A, Halmi P, Hänninen M, Hämäläinen JM, Vihinen M, Sly WS, Parkkila S (2005). "Characterization of CA XV, a new GPI-anchored form of carbonic anhydrase". Biochem. J. 392 (Pt 1): 83–92. doi:10.1042/BJ20051102. PMC 1317667. PMID 16083424.
^ ^a ^b Sawaya MR, Cannon GC, Heinhorst S, Tanaka S, Williams EB, Yeates TO, Kerfeld CA (2006). "The structure of beta-carbonic anhydrase from the carboxysomal shell reveals a distinct subclass with one active site for the price of two". J. Biol. Chem. 281 (11): 7546–55. doi:10.1074/jbc.M510464200. PMID 16407248.
^ So AK, Espie GS, Williams EB, Shively JM, Heinhorst S, Cannon GC (2004). "A novel evolutionary lineage of carbonic anhydrase (epsilon class) is a component of the carboxysome shell". J. Bacteriol. 186 (3): 623–30. doi:10.1128/JB.186.3.623-630.2004. PMC 321498. PMID 14729686.
^ ^a ^b Lane TW, Saito MA, George GN, Pickering IJ, Prince RC, Morel FM (May 2005). "Biochemistry: a cadmium enzyme from a marine diatom". Nature 435 (7038): 42. doi:10.1038/435042a. PMID 15875011. Lay summary – SSRL Science Highlight.

Eukaryotic-type carbonic anhydrase Provide feedback

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External database links

HOMSTRAD:	cah
PANDIT:	PF00194
PROSITE:	PDOC00146
Pseudofam:	PF00194
SCOP:	1can
SYSTERS:	Carb_anhydrase

This tab holds annotation information from the InterPro database.

InterPro entry IPR001148

Carbonic anhydrases (CA: EC) are zinc metalloenzymes which catalyse the reversible hydration of carbon dioxide to bicarbonate [PUBMED:18336305, PUBMED:10978542]. The alpha-CAs are found predominantly in animals but also in bacteria and green algae. There are at least 15 isoforms found in mammals, which can be subdivided into cytosolic CAs (CA-I, CA-II, CA-III, CA-VII and CA XIII), mitochondrial CAs (CA-VA and CA-VB), secreted CAs (CA-VI), membrane-associated (CA-IV, CA-IX, CA-XII and CA-XIV) and those without CA activity, the CA-related proteins (CA-RP VIII, X and XI).

This entry represents a domain characteristic of alpha class carbonic anhydrases. The dominating secondary structure is a 10-stranded, twisted beta-sheet, which divides the molecules into two halves [PUBMED:9336012]. Alpha-CAs contain a single zinc atom bound to three conserved histidine residues. The catalytically active group is the zinc-bound water which ionizes to a hydroxide group. In the mechanism of catalysis, nucleophilic attack of CO2 by a zinc-bound hydroxide ion is followed by displacement of the resulting zinc-bound bicarbonate ion by water; subsequent deprotonation regenerates the nucleophilic zinc-bound hydroxide ion [PUBMED:8673298, PUBMED:11493685].

Domain organisation

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	Seed (14)	Full (3112)	Representative proteomes				NCBI (2849)	Meta (68)
	Seed (14)	Full (3112)	RP15 (360)	RP35 (612)	RP55 (1041)	RP75 (1486)	NCBI (2849)	Meta (68)
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	Seed (14)	Full (3112)	Representative proteomes				NCBI (2849)	Meta (68)
	Seed (14)	Full (3112)	RP15 (360)	RP35 (612)	RP55 (1041)	RP75 (1486)	NCBI (2849)	Meta (68)
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	Seed (14)	Full (3112)	Representative proteomes				NCBI (2849)	Meta (68)
	Seed (14)	Full (3112)	RP15 (360)	RP35 (612)	RP55 (1041)	RP75 (1486)	NCBI (2849)	Meta (68)
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Curation

Seed source:

Prosite

Previous IDs:

carb_anhydrase;

Type:

Domain

Author:

Finn RD

Number in seed:

14

Number in full:

3112

Average length of the domain:

215.10 aa

Average identity of full alignment:

26 %

Average coverage of the sequence by the domain:

65.40 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	20.1	20.1
Trusted cut-off	20.1	20.2
Noise cut-off	19.7	19.9

Model length:

256

Family (HMM) version:

16

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Carb_anhydrase

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 Carb_anhydrase domain has been found. There are 506 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 seqence.

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Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: Carb_anhydrase (PF00194)

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Summary: Eukaryotic-type carbonic anhydrase

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Carbonic anhydrase Edit Wikipedia article

Contents

Reaction

Mechanism

CA families

α-CA

β-CA

γ-CA

δ-CA

ε-CA

Pharmacological agents affecting CA

Structure and function of carbonic anhydrase

References

Further reading

Eukaryotic-type carbonic anhydrase Provide feedback

External database links

InterPro entry IPR001148

Domain organisation

Alignments

Alignment types

Viewing

Reformatting

Downloading

View options

Format an alignment

Download options

External links

HMM logo

Trees

Curation and family details

Curation

HMM information

Species distribution

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How the sunburst is generated

Colouring and labels

Anomalies in the taxonomy tree

Missing taxonomic levels

Unmapped species names

Sub-species

Too many species/sequences

Tree controls

Annotation

Download tree

Selected sequences

Species trees

Interactive tree

Interactions

Structures