User:BQUB15-Mmarzabal/Sandbox
| Human Alkyladenine DNA Glycosylase | |||||||||
|---|---|---|---|---|---|---|---|---|---|
 Tridimensional structure simulation of hAAG associated with a double helix of DNA generated with Pymol | |||||||||
| Identifiers | |||||||||
| EC no. | 3.2.2.21 | ||||||||
| Databases | |||||||||
| IntEnz | IntEnz view | ||||||||
| BRENDA | BRENDA entry | ||||||||
| ExPASy | NiceZyme view | ||||||||
| KEGG | KEGG entry | ||||||||
| MetaCyc | metabolic pathway | ||||||||
| PRIAM | profile | ||||||||
| PDB structures | RCSB PDB PDBe PDBsum | ||||||||
| Gene Ontology | AmiGO / QuickGO | ||||||||
| |||||||||
Human Alkyladenine DNA Glycosylase (also known as hAAG), alternatively named 3-methyladenine DNA glycosylase, MPG or ANPG, is an specific type of DNA glycosylase enzyme. This type correspond to a family of monofunctional glycosylases involved in the recognition of a variety of base lesions, including alkylated and deaminated purines, and initiating their repair via the base excision repair pathway.[1] To date, hAAG is the only glycosylase identified in human cells that excises alkylation-damaged purine bases.[2]
Function
[edit]DNA bases are subject to a large number of anomalies: spontaneous alkylation or oxidative deamination. It is estimated that 104 mutations appear in a typical human cell per day. Albeit it seems to be an insignificant amount considering the extension of the DNA (1010 nucleotides), these mutations lead to changes in the structure and coding potencial of the DNA, affecting processes of replication and transcription.
Alkylation Repairing Activity
[edit]In human cells,[3] AAG is the enzyme responsible for recognition and initiation of the repair, via catalysing the hydrolysis of the N-glycosidic bond to release the alkylation-damaged purine bases.[4] Specifically, hAAG is able to efficiently identify and excise 3-methyladenine, 7-methyladenine, 7-methylguanine, 1N-ethenoadenine and hypoxanthine.[5]
ODG Activity
[edit]Oxanine DNA Glycolase (ODG) activity is the capability of some DNA Glycosylases of repairing Oxanines (Oxa), a deamined base lesion in which the N1-nitrogen is replaced by oxygen. Among the known human DNA glycosylases tested, the human alkyladenine DNA glycosylase (AAG) also shows ODG activity.[6]
Contrary to the alkylation repairing activity, which is only able to act against purine bases, the hAAG is able to excise Oxa from all of four Oxa-containing double stranded base pairs, Cyt/Oxa, Thy/Oxa, Ade/Oxa, and Gua/Oxa, showing no particular preference by any of the bases. In addition hAAG is capable of removing Oxa from single-stranded Oxa- containing DNA. This occurs because the ODG activity of the hAAG does not require a complementary strand.
Structure
[edit]Human Alkyladenine DNA Glycosylase is a monomeric protein compounded by 298 amino acids, with a formula weight of 33kDa. Its canonical primary structure consists of the following sequence. However, also other functional isoforms have been found.
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It folds into a single domain of mixed α/β structure with seven α helices and eight β strands. The core of the protein consists of a curved, antiparallel β sheet with a protruding β hairpin (β3β4) that inserts into the minor groove of the bound DNA. A series of α helices and connecting loops form the remainder of the DNA binding interface.[7] It lacks the helix-hairpin-helix motif associated with other base excision-repair proteins and, in fact, it does not resemble any other model in the Protein Data Bank.[7]
Mechanism
[edit]Substrate Recognition
[edit]Human Alkyladenine DNA Glycosylase is part of the family of enzymes that follow the BER, acting on specific substrates according to BER steps.
The process of recognition of damaged bases involves initial non-specific binding followed by diffusion along the DNA. Formed the AAG-DNA complex, it occurs a redundant process of search because of the long lifetime of this complex, while hAAG search many adjacent sites in a DNA molecule in a single binding. This provides ample opportunity to recognize and excise lesions that minimally perturb the structure of the DNA.[8]
Due to its broad specificity, the hAAG performs the substrate selection through a combination of selectivity filters.[9]
- The first selectivity filter occurs at the nucleotide flipping step of unusable base pairs that present lesions.
- The second selectivity filter is constituted by the catalytic mechanism which ensures that only purine bases are excised, even though smaller pyrimidines can fit in the hAAG’s active site. The active site pocket it’s designed to acomodate a structurally diverse set of modified purines so it would be difficult to sterically exclude the smaller pyrimidine bases from binding. However, thanks to the different shape and chemical properties of a bound pyrimidine and a purine substrate, the acid-catalyzed reacts only with the pyrymidine preventing it from binding with the hAAG.[10]
- The third selectivity filter consist of unfavorable steric clashes that allow a preferential recognition of purine lesions lacking exocyclic amino groups of guanine and adenine.
Schematic diagram of hAAG-DNA contacts
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Nucleotide Flipping and Fixation
[edit]Its structure contains an antiparallel β sheet with protruding β hairpin (β3β4) that inserts into the minor groove of the bound DNA. This group is unique for the human cells and displaces the selected nucleotide targeted for base excision by flipping it. The nucleotide is secured into the enzyme binding pocket where the active site is found, and is fixed by the amino acids Arg182, Glu125 and Ser262. Also other bonds are formed to bordering nucleotides to stabilize the structure.
The groove in the double helix of DNA left by the flipped-out abasic nucleotide is filled with the lateral chain of the amino acid Tyr162, making no specific contacts with the surrounding bases.
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Nucleotide Release
[edit]Activated by nearby aminoacids, a water molecule attacks the N-Glycosydic bound releasing the alkylated base via a backside displacement mechanism.
Location
[edit]Human Alkyladenine DNA Glycosylase localizes to the mitochondria, nucleus and cytoplasm of human cells.[11] Despite only being found in human cells, some functionally equivalent enzymes have been found in other spieces, but with significantly different structures, such as E. coli DNA-3-methyladenine glycosylase.[7]
Pathology
[edit]According to the mechanism used by Human Alkyladenine DNA Glycosylase, a defect in the DNA repair pathways lead to cancer predisposition. HAAG follows the BER steps so that means that an incorrect role of BER genes could contribute to the development of cancer. Concretely, a bad activity of hAAG may be associated with cancer risk in BRCA1 and BRCA2 mutation carriers.[12]
References
[edit]- ^ Hedglin, Mark; O'Brien, Patrick J. (2008) "Human Alkyladenine DNA Glycosylase employs a processive search for dNA damage". Biochemistry 47: 11434-11445.
- ^ Abner, Clint W.; Lau, Albert Y.; Ellenberger, Tom; Bloom, Linda B. (2001-04-20). "Base Excision and DNA Binding Activities of Human Alkyladenine DNA Glycosylase Are Sensitive to the Base Paired with a Lesion". Journal of Biological Chemistry. 276 (16): 13379–13387. doi:10.1074/jbc.M010641200. ISSN 0021-9258. PMID 11278716.
{{cite journal}}: CS1 maint: unflagged free DOI (link) - ^ O'Brie, Patrick J.; Ellenberger, Tom. "Human Alkyladenine DNA Glycosylase Uses Acid−Base Catalysis for Selective Excision of Damaged Purines †". Biochemistry. 42 (42): 12418–12429. doi:10.1021/bi035177v.
- ^ Admiraal, Suzanne J.; O'Brien, Patrick J. (2010-10-26). "N-Glycosyl Bond Formation Catalyzed by Human Alkyladenine DNA Glycosylase". Biochemistry. 49 (42): 9024–9026. doi:10.1021/bi101380d. ISSN 0006-2960. PMC 2975558. PMID 20873830.
- ^ Hollis, Thomas; Lau, Albert; Ellenberger, Tom (2000-08-30). "Structural studies of human alkyladenine glycosylase and E. coli 3-methyladenine glycosylase". Mutation Research/DNA Repair. 460 (3–4): 201–210. doi:10.1016/S0921-8777(00)00027-6.
- ^ Hitchcock, Thomas M.; Dong, Liang; Connor, Ellen E.; Meira, Lisiane B.; Samson, Leona D.; Wyatt, Michael D.; Cao, Weiguo (September 10, 2004). "Oxanine DNA Glycosylase Activity from Mammalian Alkyladenine Glycosylase". THE JOURNAL OF BIOLOGICAL CHEMISTRY. Vol. 279 (No. 37).
{{cite journal}}:|issue=has extra text (help);|volume=has extra text (help) - ^ a b c Lau, Albert Y.; Schärer, Orlando D.; Samson, Leona; Verdine, Gregory L.; Ellenberger, Tom. "Crystal Structure of a Human Alkylbase-DNA Repair Enzyme Complexed to DNA". Cell. 95 (2): 249–258. doi:10.1016/S0092-8674(00)81755-9. ISSN 0092-8674. PMID 9790531.
- ^ Zhang, Yaru. "Specificity and Searching Mechanism of Alkyladenine DNA Glycosylase".
- ^ Hedglin, Mark; O'Brien, Patrick J. (2008) "Human Alkyladenine DNA Glycosylase employs a processive search for dNA damage". Biochemistry 47: 11434-11445.
- ^ O'Brie, Patrick J.; Ellenberger, Tom. "Human Alkyladenine DNA Glycosylase Uses Acid−Base Catalysis for Selective Excision of Damaged Purines †". Biochemistry. 42 (42): 12418–12429. doi:10.1021/bi035177v.
- ^ van Loon, Barbara; Samson, Leona D. (2013-03-01). "Alkyladenine DNA glycosylase (AAG) localizes to mitochondria and interacts with mitochondrial single-stranded binding protein (mtSSB)". DNA repair. 12 (3): 177–187. doi:10.1016/j.dnarep.2012.11.009. ISSN 1568-7864. PMC 3998512. PMID 23290262.
- ^ Osorio, Ana; Milne, Roger L.; Kuchenbaecker, Karoline; Vaclová, Tereza; Pita, Guillermo; Alonso, Rosario; Peterlongo, Paolo; Blanco, Ignacio; de la Hoya, Miguel (2014-04-03). "DNA Glycosylases Involved in Base Excision Repair May Be Associated with Cancer Risk in BRCA1 and BRCA2 Mutation Carriers". PLoS Genetics. 10 (4). doi:10.1371/journal.pgen.1004256. ISSN 1553-7390. PMC 3974638. PMID 24698998.
{{cite journal}}: CS1 maint: unflagged free DOI (link)