DNA-3-methyladenine glycosylase

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MPG
Protein MPG PDB 1bnk.png
Available structures
PDB Ortholog search: PDBe RCSB
Identifiers
Aliases MPG, AAG, ADPG, APNG, CRA36.1, MDG, Mid1, PIG11, PIG16, anpg, N-methylpurine DNA glycosylase
External IDs MGI: 97073 HomoloGene: 1824 GeneCards: MPG
RNA expression pattern
PBB GE MPG 203686 at fs.png
More reference expression data
Orthologs
Species Human Mouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

NM_002434
NM_001015052
NM_001015054

NM_010822

RefSeq (protein)

NP_001015052
NP_001015054
NP_002425

NP_034952.2
NP_034952

Location (UCSC) Chr 16: 0.08 – 0.09 Mb Chr 11: 32.23 – 32.23 Mb
PubMed search [1] [2]
Wikidata
View/Edit Human View/Edit Mouse

DNA-3-methyladenine glycosylase also known as 3-alkyladenine DNA glycosylase (AAG) or N-methylpurine DNA glycosylase (MPG) is an enzyme that in humans is encoded by the MPG gene.[3][4]

Alkyladenine DNA glycosylase is a specific type of DNA glycosylase. This subfamily of monofunctional glycosylases is 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.[5] To date, the human AAG (hAAG) is the only glycosylase identified that excises alkylation-damaged purine bases.[6]

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 potential of the DNA, affecting processes of replication and transcription.

3-Methyladenine DNA glycosilases are able to initiate the base excision repair (BER) of a wide range of substrate bases that, due to their chemical reactivity, suffer inevitable modifications resulting in different biological outcomes. DNA repair mechanisms take on a vital role in maintaining the genomic integrity of cells from different organisms, in particular 3-Methyladenine DNA glycosylases are found in bacteria, yeast, plants, rodents and humans. Therefore, there are different subfamilies of this enzyme, such as the Human Alkyladenine DNA Glycosylase (hAAG), that act on other damaged DNA bases apart from 3-MeA [7]

Table that shows the presence (+) or absence (-) of biochemical activity between the different subfamilies of the DNA-3-methyladenine glycosylase and the different types of damaged DNA bases
tag AlkA MAG mag1 ADPG Aag AGG aMAG
3-MeA + + + + + + + +
3-MeG + + + + + +
7-MeG - + + + + + + +
O2-MeG - +
O2-MeC - +
7-CEG + +
7-HEG + +
7-EthoxyG +
eA - + + + + + +
eG +
8-oxoG + +
Hx - + + + + + +
A + +
G - + + + +
T +
C +

Alkylation repairing activity[edit]

In cells,[8] 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.[9] Specifically, hAAG is able to efficiently identify and excise 3-methyladenine, 7-methyladenine, 7-methylguanine, 1N-ethenoadenine and hypoxanthine.[10]

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.[11]

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]

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.

Human Alkyladenine DNA Glycosylase Sequence or Isoform 1
PDB rendering based on 1F6O
Human Alkyladenine DNA Glycosylase's structure generated with Pymol

Isoform 2[edit]

The sequence of this isoform differs from the canonical sequence as follows:

Aminoacids 1-12: MVTPALQMKKPK → MPARSGA

Aminoacids 195-196: QL →HV

Isoform 3[edit]

The sequence of this isoform differs from the canonical sequence in a similar way as the isoform 2:

Aminoacids 1-12: MVTPALQMKKPK → MPARSGA

Isoform 4[edit]

The sequence of this isoform misses the aminoacids 1-17.

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.[12] 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.[12]

Mechanism[edit]

Substrate recognition[edit]

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, a redundant process of search occurs 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.[13]

Due to its broad specificity, the hAAG performs the substrate selection through a combination of selectivity filters.[14]

  • 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 accommodate 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.[8]
  • 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

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.

N-Glycosidic bond cleavage by Human Alkyladenine DNA Glycosylase

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.[15] Despite only being found in human cells, some functionally equivalent enzymes have been found in other species, but with significantly different structures, such as E. coli DNA-3-methyladenine glycosylase.[12]

Clinical significance[edit]

According to the mechanism used by Human Alkyladenine DNA Glycosylase, a defect in the DNA repair pathways leads 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.[16]

Model organisms[edit]

Model organisms have been used in the study of MPG function. A conditional knockout mouse line called Mpgtm1a(EUCOMM)Wtsi was generated at the Wellcome Trust Sanger Institute.[17] Male and female animals underwent a standardized phenotypic screen[18] to determine the effects of deletion.[19][20][21][22] Additional screens performed: - In-depth immunological phenotyping[23]

See also[edit]

References[edit]

  1. ^ "Human PubMed Reference:". 
  2. ^ "Mouse PubMed Reference:". 
  3. ^ Chakravarti D, Ibeanu GC, Tano K, Mitra S (Aug 1991). "Cloning and expression in Escherichia coli of a human cDNA encoding the DNA repair protein N-methylpurine-DNA glycosylase". The Journal of Biological Chemistry. 266 (24): 15710–5. PMID 1874728. 
  4. ^ "Entrez Gene: MPG N-methylpurine-DNA glycosylase". 
  5. ^ Hedglin M, O'Brien PJ (2008). "Human alkyladenine DNA glycosylase employs a processive search for DNA damage". Biochemistry. 47 (44): 11434–45. doi:10.1021/bi801046y. PMC 2702167Freely accessible. PMID 18839966. 
  6. ^ Abner CW, Lau AY, Ellenberger T, Bloom LB (Apr 2001). "Base excision and DNA binding activities of human alkyladenine DNA glycosylase are sensitive to the base paired with a lesion". The Journal of Biological Chemistry. 276 (16): 13379–87. doi:10.1074/jbc.M010641200. PMID 11278716. 
  7. ^ Wyatt, M. D.; Allan, J. M.; Lau, A. Y.; Ellenberger, T. E.; Samson, L. D. (1999-08-01). "3-methyladenine DNA glycosylases: structure, function, and biological importance". BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology. 21 (8): 668–676. doi:10.1002/(SICI)1521-1878(199908)21:8<668::AID-BIES6>3.0.CO;2-D. ISSN 0265-9247. PMID 10440863. 
  8. ^ a b O'Brien PJ, Ellenberger T (Oct 2003). "Human alkyladenine DNA glycosylase uses acid-base catalysis for selective excision of damaged purines". Biochemistry. 42 (42): 12418–29. doi:10.1021/bi035177v. PMID 14567703. 
  9. ^ Admiraal SJ, O'Brien PJ (Oct 2010). "N-glycosyl bond formation catalyzed by human alkyladenine DNA glycosylase". Biochemistry. 49 (42): 9024–6. doi:10.1021/bi101380d. PMC 2975558Freely accessible. PMID 20873830. 
  10. ^ Hollis T, Lau A, Ellenberger T (Aug 2000). "Structural studies of human alkyladenine glycosylase and E. coli 3-methyladenine glycosylase". Mutation Research. 460 (3–4): 201–10. doi:10.1016/S0921-8777(00)00027-6. PMID 10946229. 
  11. ^ Hitchcock TM, Dong L, Connor EE, Meira LB, Samson LD, Wyatt MD, Cao W (Sep 2004). "Oxanine DNA glycosylase activity from Mammalian alkyladenine glycosylase". The Journal of Biological Chemistry. 279 (37): 38177–83. doi:10.1074/jbc.M405882200. PMID 15247209. 
  12. ^ a b c Lau AY, Schärer OD, Samson L, Verdine GL, Ellenberger T (Oct 1998). "Crystal structure of a human alkylbase-DNA repair enzyme complexed to DNA: mechanisms for nucleotide flipping and base excision". Cell. 95 (2): 249–58. doi:10.1016/S0092-8674(00)81755-9. PMID 9790531. 
  13. ^ Zhang, Yaru. "Specificity and Searching Mechanism of Alkyladenine DNA Glycosylase.". 
  14. ^ Hedglin M, O'Brien PJ (2008). "Human Alkyladenine DNA Glycosylase employs a processive search for dNA damage". Biochemistry. 47: 11434–11445. doi:10.1021/bi801046y. PMC 2702167Freely accessible. PMID 18839966. 
  15. ^ van Loon B, Samson LD (Mar 2013). "Alkyladenine DNA glycosylase (AAG) localizes to mitochondria and interacts with mitochondrial single-stranded binding protein (mtSSB)". DNA Repair. 12 (3): 177–87. doi:10.1016/j.dnarep.2012.11.009. PMC 3998512Freely accessible. PMID 23290262. 
  16. ^ Osorio A, Milne RL, Kuchenbaecker K, Vaclová T, Pita G, Alonso R, et al. (Apr 2014). "DNA glycosylases involved in base excision repair may be associated with cancer risk in BRCA1 and BRCA2 mutation carriers". PLoS Genetics. 10 (4): e1004256. doi:10.1371/journal.pgen.1004256. PMC 3974638Freely accessible. PMID 24698998. 
  17. ^ Gerdin AK (2010). "The Sanger Mouse Genetics Programme: high throughput characterisation of knockout mice". Acta Ophthalmologica. 88: 925–7. doi:10.1111/j.1755-3768.2010.4142.x. 
  18. ^ a b "International Mouse Phenotyping Consortium". 
  19. ^ Skarnes WC, Rosen B, West AP, Koutsourakis M, Bushell W, Iyer V, Mujica AO, Thomas M, Harrow J, Cox T, Jackson D, Severin J, Biggs P, Fu J, Nefedov M, de Jong PJ, Stewart AF, Bradley A (Jun 2011). "A conditional knockout resource for the genome-wide study of mouse gene function". Nature. 474 (7351): 337–42. doi:10.1038/nature10163. PMC 3572410Freely accessible. PMID 21677750. 
  20. ^ Dolgin E (Jun 2011). "Mouse library set to be knockout". Nature. 474 (7351): 262–3. doi:10.1038/474262a. PMID 21677718. 
  21. ^ Collins FS, Rossant J, Wurst W (Jan 2007). "A mouse for all reasons". Cell. 128 (1): 9–13. doi:10.1016/j.cell.2006.12.018. PMID 17218247. 
  22. ^ White JK, Gerdin AK, Karp NA, Ryder E, Buljan M, Bussell JN, et al. (Jul 2013). "Genome-wide generation and systematic phenotyping of knockout mice reveals new roles for many genes". Cell. 154 (2): 452–64. doi:10.1016/j.cell.2013.06.022. PMC 3717207Freely accessible. PMID 23870131. 
  23. ^ a b "Infection and Immunity Immunophenotyping (3i) Consortium". 

Further reading[edit]

External links[edit]