Biology:5'-deoxyadenosine deaminase
5'-deoxyadenosine deaminase (also known as "DadD") is an enzyme that catalyzes the conversion of 5′-deoxyadenosine to 5′-deoxyinosine.[1][2] To a lesser extent, the enzyme also catalyzes the deamination of 5′-methylthioadenosine, S-adenosylhomocysteine, and adenosine.[1] The molecular mass of the DadD enzyme is approximately 230 kDa.[1] DadD maintains 90% of its enzymatic activity after being heated at 60 degrees Celsius for ten minutes.[1] The preferred pH for 5'deoxyadenosine deaminase is 9.0, with the enzyme denaturing at a pH of 11.[1] The DadD enzyme has a preferred substrate of 5'deoxyadenosine, though it will also react with 5′-methylthioadenosine, S-adenosylhomocysteine, and adenosine at lower efficiencies.[1]
Enzyme identification
The EC number of 5'-deoxyadenosine deaminase is EC:3.5.4.41.[1] The Enzyme Commission Number is a system of classifying enzymes based on the reactions that the enzyme catalyzes.[3] Due to EC number not being attached to specific enzymes, but rather the enzyme catalyzed reaction, a single EC number could describe a variety of enzymes that catalyze the same reaction.[4] The UniProt id number for 5'-deoxyadenosine deaminase is Q58936. This number is specific to the enzyme itself, not just the reaction it catalyzes.
Reaction pathway
5'-deoxyadenosine deaminase catalyses the salvage pathway of 5'-deoxyadenosine to 5'-deoxyinosine following the reaction pathway of [math]\ce{ C10H13N5O3 + H+ + H2O <=>> C10H12N4O4 + NH4+ }[/math].[1][5] In this reaction 5'-deoxyadenosine is converted to 5'-deoxyinosine with ammonia as a byproduct.[1][5]
Structure
The enzyme has many active sites, with some of them specifically being metal binding sites that interact with zinc.[1] The metal binding sites are located at positions 55, 57, 203, and 292.[5] Additional binding sites include positions 84, 176, 206, and 292.[5] The solved crystal structure of 5'-deoxyadenosine deaminase can be found in the SMR database here.
Variation across species
The DadD enzyme is unique in that it has only been discovered in a single organism; a thermophilic methanogenic archaean named Methanocaldococcus jannaschii.[1] In methanogens such as Methanocaldococcus jannaschii, the typical metabolism pathway of salvaging radical SAM reaction products cannot be used, due to a lack of the enzyme MTA/SAH nucleosidase (EC 3.2.2.9).[1] Salvaging radical SAM reaction products is important for methanogens.[1] Without a salvage pathway, 5'-deoxyadenosine would build up, and inhibit the processes of biotin synthase (BioB) and lipoyl synthase (LipA).[1][6] The DadD enzyme offers a mechanism for methanogens to salvage these SAM reaction products without the use of MTA/SAH nucleosidase.[1]
References
- ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 1.14 Miller, D.; O'Brien, K.; Xu, H.; White, R. H. (2013-12-27). "Identification of a 5'-Deoxyadenosine Deaminase in Methanocaldococcus jannaschii and Its Possible Role in Recycling the Radical S-Adenosylmethionine Enzyme Reaction Product 5'-Deoxyadenosine". Journal of Bacteriology 196 (5): 1064–1072. doi:10.1128/jb.01308-13. ISSN 0021-9193. PMID 24375099.
- ↑ "BRENDA - Information on EC 3.5.4.41 - 5'-deoxyadenosine deaminase". BRENDA. https://www.brenda-enzymes.org/enzyme.php?ecno=3.5.4.41."BRENDA - Information on EC 3.5.4.41 - 5'-deoxyadenosine deaminase". BRENDA. https://www.brenda-enzymes.org/enzyme.php?ecno=3.5.4.41.
- ↑ "Nomenclature Committee of the International Union of Biochemistry and Molecular Biology", Enzyme Nomenclature, Elsevier, 1992, pp. ii, doi:10.1016/b978-0-12-227164-9.50001-7, ISBN 9780122271649, https://archive.org/details/enzymenomenclatu0000inte_d6c2/page/
- ↑ "ExPaSy (Expert Protein Analysis System)", Encyclopedic Dictionary of Genetics, Genomics and Proteomics, John Wiley & Sons, Inc., 2004-07-15, doi:10.1002/0471684228.egp04300, ISBN 0471684228
- ↑ 5.0 5.1 5.2 5.3 "dadD - 5'-deoxyadenosine deaminase - Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) - dadD gene & protein". https://www.uniprot.org/uniprot/Q58936.
- ↑ Booker, Squire J (2010-07-15). "Mechanistic and functional versatility of radical SAM enzymes". F1000 Biology Reports 2: 52. doi:10.3410/b2-52. ISSN 1757-594X. PMID 21152342.
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