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2  structures 275  species 1  interaction 781  sequences 25  architectures

Family: A_deamin (PF02137)

Summary: Adenosine-deaminase (editase) domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Adenosine deaminase". More...

Adenosine deaminase Edit Wikipedia article

Adenosine deaminase
Adenosine deaminase 1VFL.png
Ribbon diagram of bovine adenosine deaminase. Zinc ion visible at center. From PDB 1VFL
Available structures
PDB Ortholog search: PDBe, RCSB
Identifiers
Symbol ADA
External IDs OMIM608958 MGI87916 HomoloGene37249 ChEMBL: 1910 GeneCards: ADA Gene
EC number 3.5.4.4
RNA expression pattern
PBB GE ADA 204639 at tn.png
PBB GE ADA 216705 s at tn.png
More reference expression data
Orthologs
Species Human Mouse
Entrez 100 11486
Ensembl ENSG00000196839 ENSMUSG00000017697
UniProt P00813 P03958
RefSeq (mRNA) NM_000022 NM_001272052
RefSeq (protein) NP_000013 NP_001258981
Location (UCSC) Chr 20:
43.25 – 43.28 Mb
Chr 2:
163.73 – 163.75 Mb
PubMed search [1] [2]
Adenosine/AMP deaminase
PDB 2amx EBI.jpg
crystal structure of plasmodium yoelii adenosine deaminase (py02076)
Identifiers
Symbol A_deaminase
Pfam PF00962
Pfam clan CL0034
InterPro IPR001365
PROSITE PDOC00419
SCOP 1add
SUPERFAMILY 1add
Adenosine deaminase (editase) domain
Identifiers
Symbol A_deamin
Pfam PF02137
InterPro IPR002466
PROSITE PDOC00419
SCOP 1add
SUPERFAMILY 1add
Adenosine/AMP deaminase N-terminal
Identifiers
Symbol A_deaminase_N
Pfam PF08451
InterPro IPR013659

Adenosine deaminase (also known as adenosine aminhydrolase, or ADA) is an enzyme (EC 3.5.4.4) involved in purine metabolism. It is needed for the breakdown of adenosine from food and for the turnover of nucleic acids in tissues.

Present in virtually all mammalian cells, its primary function in humans is the development and maintenance of the immune system.[1] However, the full physiological role of ADA is not yet completely understood.[2]

Structure

ADA exists in both small form (as a monomer) and large form (as a dimer-complex).[2] In the monomer form, the enzyme is a polypeptide chain,[3] folded into eight strands of parallel α/β barrels, which surround a central deep pocket that is the active site.[1] In addition to the eight central β-barrels and eight peripheral α-helices, ADA also contains five additional helices: residues 19-76 fold into three helices, located between β1 and α1 folds; and two antiparallel carboxy-terminal helices are located across the amino-terminal of the β-barrel.

The ADA active site contains a zinc ion, which is located in the deepest recess of the active site and coordinated by five atoms from His15, His17, His214, Asp295, and the substrate.[1] Zinc is the only cofactor necessary for activity.

The substrate, adenosine, is stabilized and bound to the active site by nine hydrogen bonds.[1] The carboxyl group of Glu217, roughly coplanar with the substrate purine ring, is in position to form a hydrogen bond with N1 of the substrate. The carboxyl group of Asp296, also coplanar with the substrate purine ring, forms hydrogen bond with N7 of the substrate. The NH group of Gly184 is in position to form a hydrogen bond with N3 of the substrate. Asp296 forms bonds both with the Zn2+ ion as well as with 6-OH of the substrate. His238 also hydrogen bonds to substrate 6-OH. The 3'-OH of the substrate ribose forms a hydrogen bond with Asp19, while the 5'-OH forms a hydrogen bond with His17. Two further hydrogen bonds are formed to water molecules, at the opening of the active site, by the 2'-OH and 3'-OH of the substrate.

Due to the recessing of the active inside the enzyme, the substrate once bound is almost completely sequestered from solvent.[1] The surface exposure of the substrate to solvent when bound is 0.5% the surface exposure of the substrate in the free state.

Reactions

ADA irreversibly deaminates adenosine, converting it to the related nucleoside inosine by the substitution of the amino group for a hydroxyl group.

Adenosine
Inosine

Inosine can then be deribosylated (removed from ribose) by another enzyme called purine nucleoside phosphorylase (PNP), converting it to hypoxanthine.

Mechanism

Two proposed mechanism exist for ADA-catalyzed deamination: 1) stereospecific addition-elimination via tetrahedral intermediate or 2) an SN2 reaction.[2][4] By either mechanism, Zn2+ as a strong electrophile activates a water molecule, which is deprotonated by the basic Asp295 to form the attacking hydroxide.[1] His238 orients the water molecule and stabilizes the charge of the attacking hydroxide. Glu217 is protonated to donate a proton to N1 of the substrate.

The reaction is stereospecific due to the location of the zinc, Asp295, and His238 residues, which all face the B-side of the purine ring of the substrate.[1]

Competitive inhibition has been observed for ADA, where the product inosine acts at the competitive inhibitor to enzymatic activity.[5]

Biological Function

ADA is considered one of the key enzymes of purine metabolism.[4] The enzyme has been found in bacteria, plants, invertebrates, vertebrates, and mammals, with high conservation of amino acid sequence.[2] The high degree of amino acid sequence conservation suggests the crucial nature of ADA in the purine salvage pathway.

Primarily, ADA in humans is involved in the development and maintenance of the immune system. However, ADA association has also been observed with epithelial cell differentiation, neurotransmission, and gestation maintenance.[6] It has also been proposed that ADA, in addition to adenosine breakdown, stimulates release of excitatory amino acids and is necessary to the coupling of A1 adenosine receptors and heterotrimeric G proteins.[2]

Pathology

Some mutations in the gene for adenosine deaminase cause it not to be expressed. The resulting deficiency is one cause of severe combined immunodeficiency (SCID).[7] Deficient levels of ADA have also been associated with pulmonary inflammation, thymic cell death, and defective T-cell receptor signaling.[8][9]

Conversely, mutations causing this enzyme to be overexpressed are one cause of hemolytic anemia .[10]

There is some evidence that a different allele (ADA2) may lead to autism.[11]

Elevated levels of ADA has also been associated with AIDS.[8][12]

Isoforms

There are 2 isoforms of ADA: ADA1 and ADA2.

  • ADA1 is found in most body cells, particularly lymphocytes and macrophages, where it is present not only in the cytosol and nucleus but also as the ecto- form on the cell membrane attached to dipeptidyl peptidase-4 (aka, CD26). ADA1 is involved mostly in intracellular activity, and exists both in small form (monomer) and large form (dimer).[2] The interconversion of small to large forms is regulated by a 'conversion factor' in the lung.[13]
  • ADA2 was first identified in human spleen.[14] It was subsequently found in other tissues including the macrophage where it co-exists with ADA1. The two isoforms regulate the ratio of adenosine to deoxyadenosine potentiating the killing of parasites. ADA2 is found predominantly in the human plasma and serum, and exists solely as a homodimer.[15]

Clinical significance

ADA2 is the predominant form present in human blood plasma and is increased in many diseases, particularly those associated with the immune system: for example rheumatoid arthritis, psoriasis, and sarcoidosis. The plasma ADA2 isoform is also increased in most cancers. ADA2 is not ubiquitous but co-exists with ADA1 only in monocytes-macrophages.[citation needed]

Total plasma ADA can be measured using high performance liquid chromatography or enzymatic or colorimetric techniques. Perhaps the simplest system is the measurement of the ammonia released from adenosine when broken down to inosine. After incubation of plasma with a buffered solution of adenosine the ammonia is reacted with a Berthelot reagent to form a blue colour which is proportionate to the amount of enzyme activity. To measure ADA2, erythro-9-(2-hydroxy-3-nonyl) adenine (EHNA) is added prior to incubation so as to inhibit the enzymatic activity of ADA1.[14] It is the absence of ADA1 that causes SCID.

ADA can also be used in the workup of lymphocytic pleural effusions or peritoneal ascites, in that such specimens with low ADA levels essentially excludes tuberculosis from consideration.[17]

Tuberculosis pleural effusions can now be diagnosed accurately by increased levels of pleural fluid adenosine deaminase, above 40 U per liter.[18]

Cladribine is an anti-neoplastic agent used in the treatment of hairy cell leukemia; its mechanism of action is inhibition of adenosine deaminase.

See also

References

  1. ^ a b c d e f g Wilson, D. K.; Rudolph, F. B.; Quiocho, F. A. (1991). "Atomic structure of adenosine deaminase complexed with a transition-state analog: Understanding catalysis and immunodeficiency mutations". Science 252 (5010): 1278–1284. doi:10.1126/science.1925539. PMID 1925539.  edit
  2. ^ a b c d e f Cristalli, G.; Costanzi, S.; Lambertucci, C.; Lupidi, G.; Vittori, S.; Volpini, R.; Camaioni, E. (2001). "Adenosine deaminase: Functional implications and different classes of inhibitors". Medicinal Research Reviews 21 (2): 105–128. doi:10.1002/1098-1128(200103)21:2<105::AID-MED1002>3.0.CO;2-U. PMID 11223861.  edit
  3. ^ Daddona, P. E.; Kelley, W. N. (1977). "Human adenosine deaminase. Purification and subunit structure". The Journal of Biological Chemistry 252 (1): 110–115. PMID 13062.  edit
  4. ^ a b Glader, B. E.; Backer, K.; Diamond, L. K. (1983). "Elevated Erythrocyte Adenosine Deaminase Activity in Congenital Hypoplastic Anemia". New England Journal of Medicine 309 (24): 1486–1490. doi:10.1056/NEJM198312153092404. PMID 6646173.  edit
  5. ^ Saboury, A. A.; Divsalar, A.; Jafari, G. A.; Moosavi-Movahedi, A. A.; Housaindokht, M. R.; Hakimelahi, G. H. (2002). "A product inhibition study on adenosine deaminase by spectroscopy and calorimetry". Journal of biochemistry and molecular biology 35 (3): 302–305. doi:10.5483/BMBRep.2002.35.3.302. PMID 12297022.  edit
  6. ^ Moriwaki, Y.; Yamamoto, T.; Higashino, K. (1999). "Enzymes involved in purine metabolism--a review of histochemical localization and functional implications". Histology and histopathology 14 (4): 1321–1340. PMID 10506947.  edit
  7. ^ Sanchez JJ, Monaghan G, Børsting C, Norbury G, Morling N, Gaspar HB (2007). "Carrier frequency of a nonsense mutation in the adenosine deaminase (ADA) gene implies a high incidence of ADA-deficient severe combined immunodeficiency (SCID) in Somalia and a single, common haplotype indicates common ancestry". Ann. Hum. Genet. 71 (Pt 3): 336–47. doi:10.1111/j.1469-1809.2006.00338.x. PMID 17181544. 
  8. ^ a b Blackburn, M. R.; Kellems, R. E. (2005). Adenosine Deaminase Deficiency: Metabolic Basis of Immune Deficiency and Pulmonary Inflammation. "Advances in Immunology Volume 86". Advances in immunology. Advances in Immunology 86: 1–41. doi:10.1016/S0065-2776(04)86001-2. ISBN 9780120044863. PMID 15705418.  edit
  9. ^ Apasov, S. G.; Blackburn, M. R.; Kellems, R. E.; Smith, P. T.; Sitkovsky, M. V. (2001). "Adenosine deaminase deficiency increases thymic apoptosis and causes defective T cell receptor signaling". Journal of Clinical Investigation 108 (1): 131–141. doi:10.1172/JCI10360. PMC 209335. PMID 11435465.  edit
  10. ^ Chottiner EG, Cloft HJ, Tartaglia AP, Mitchell BS (1987). "Elevated adenosine deaminase activity and hereditary hemolytic anemia. Evidence for abnormal translational control of protein synthesis". J. Clin. Invest. 79 (3): 1001–5. doi:10.1172/JCI112866. PMC 424261. PMID 3029177. 
  11. ^ Persico AM, Militerni R, Bravaccio C, et al. (2000). "Adenosine deaminase alleles and autistic disorder: case-control and family-based association studies". Am. J. Med. Genet. 96 (6): 784–90. doi:10.1002/1096-8628(20001204)96:6<784::AID-AJMG18>3.0.CO;2-7. PMID 11121182. 
  12. ^ Cowan, M. J.; Brady, R. O.; Widder, K. J. (1986). "Elevated erythrocyte adenosine deaminase activity in patients with acquired immunodeficiency syndrome". Proceedings of the National Academy of Sciences of the United States of America 83 (4): 1089–1091. doi:10.1073/pnas.83.4.1089. PMC 323016. PMID 3006027.  edit
  13. ^ Schrader, W. P.; Stacy, A. R. (1977). "Purification and subunit structure of adenosine deaminase from human kidney". The Journal of Biological Chemistry 252 (18): 6409–6415. PMID 893413.  edit
  14. ^ a b Schrader WP, Pollara B, Meuwissen HJ (January 1978). "Characterization of the residual adenosine deaminating activity in the spleen of a patient with combined immunodeficiency disease and adenosine deaminase deficiency". Proc. Natl. Acad. Sci. U.S.A. 75 (1): 446–50. doi:10.1073/pnas.75.1.446. PMC 411266. PMID 24216. 
  15. ^ Zavialov AV, Engstrom A (Oct 2005). "Human ADA2 belongs to a new family of growth factors with adenosine deaminase activity". Biochem. J. 391 (1): 51–57. doi:10.1042/BJ20050683. PMC 1237138. PMID 15926889. 
  16. ^ Keegan LP, Leroy A, Sproul D, O'Connell MA (2004). "Adenosine deaminases acting on RNA (ADARs): RNA-editing enzymes". Genome Biol. 5 (2): 209. doi:10.1186/gb-2004-5-2-209. PMC 395743. PMID 14759252. 
  17. ^ http://erj.ersjournals.com/cgi/content/abstract/21/2/220
  18. ^ Schwartz's principles of surgery, 8th edition, self assessment and board review, chapter 18 question 16

Further reading

External links

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Adenosine-deaminase (editase) domain Provide feedback

Adenosine deaminases acting on RNA (ADARs) can deaminate adenosine to form inosine. In long double-stranded RNA, this process is non-specific; it occurs site-specifically in RNA transcripts. The former is important in defence against viruses, whereas the latter may affect splicing or untranslated regions. They are primarily nuclear proteins, but a longer isoform of ADAR1 is found predominantly in the cytoplasm. ADARs are derived from the Tad1-like tRNA deaminases that are present across eukaryotes. These in turn belong to the nucleotide/nucleic acid deaminase superfamily and are characterized by a distinct insert between the two conserved cysteines that are involved in binding zinc [2].

Literature references

  1. Keegan LP, Leroy A, Sproul D, O'Connell MA; , Genome Biol 2004;5:209.: Adenosine deaminases acting on RNA (ADARs): RNA-editing enzymes. PUBMED:14759252 EPMC:14759252

  2. Iyer LM, Zhang D, Rogozin IB, Aravind L;, Nucleic Acids Res. 2011; [Epub ahead of print]: Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems. PUBMED:21890906 EPMC:21890906


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002466

Editase (EC) are enzymes that alter mRNA by catalyzing the site-selective deamination of adenosine residue into inosine residue. The editase domain contains the active site and binds three Zn atoms [PUBMED:9159072]. Several editases share a common global arrangement of domains, from N to C terminus: two 'double-stranded RNA-specific adenosine deaminase' (DRADA) repeat domains (INTERPRO), followed by three 'double-stranded RNA binding' (DsRBD) domains (INTERPRO), followed by the editase domain. Other editases have a simplified domains structure with no DRADA_REP and possibly fewer DSRBD domains. Editase that deaminate cytidine are not detected by this signature.

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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Pfam Clan

This family is a member of clan CDA (CL0109), which has the following description:

This clan contains both free nucleotide and nucleic acid deaminases that act on adenosine, cytosine, guanine and cytidine, and are collectively known as the deaminase superfamily. The conserved fold consists of a three-layered alpha/beta/alpha structure with 3 helices and 4 strands in the 2134 order [1,2].This superfamily is further divided into two major divisions based on the presence of a helix (helix-4) that renders the terminal strands (strands 4 and 5) either parallel to each other in its presence, or anti-parallel in its absence [2]. Structurally, the deaminase-like fold is present in four other superfamilies including the JAB-like metalloproteins, the C-terminal AICAR transformylase-catalyzing domains of PurH, Tm1506 and the formate dehydrogenase accessory subunit FdhD. The active site of the deaminases is composed of three residues that coordinate a zinc ion between conserved helices 2 and 3. The residues are typically found as [HCD]xE and CxxC motifs at the beginning of helices 2 and 3. The zinc ion activates a water molecule, which forms a tetrahderal intermediate with the carbon atom that is linked to the amine group. This is followed by deamination of the base.

The clan contains the following 16 members:

A_deamin AICARFT_IMPCHas APOBEC_C APOBEC_N Bd3614-deam dCMP_cyt_deam_1 dCMP_cyt_deam_2 DYW_deaminase LmjF365940-deam MafB19-deam OTT_1508_deam Pput2613-deam SCP1201-deam Toxin-deaminase XOO_2897-deam YwqJ-deaminase

Alignments

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(59)
Full
(781)
Representative proteomes NCBI
(770)
Meta
(16)
RP15
(123)
RP35
(188)
RP55
(317)
RP75
(446)
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  Seed
(59)
Full
(781)
Representative proteomes NCBI
(770)
Meta
(16)
RP15
(123)
RP35
(188)
RP55
(317)
RP75
(446)
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  Seed
(59)
Full
(781)
Representative proteomes NCBI
(770)
Meta
(16)
RP15
(123)
RP35
(188)
RP55
(317)
RP75
(446)
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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: IPR002466
Previous IDs: none
Type: Family
Author: Mian N, Bateman A, Iyer LM, Zhang D, Aravind L
Number in seed: 59
Number in full: 781
Average length of the domain: 308.00 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 55.17 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 19.8 19.8
Trusted cut-off 21.2 19.9
Noise cut-off 18.9 18.6
Model length: 343
Family (HMM) version: 13
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Species distribution

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Interactions

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A_deamin

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 A_deamin domain has been found. There are 2 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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