DNA Glycosylases

 

Table of Contents:

DNA Glycosylases Introduction Classifications Examples  Medical Importance

 

 

Introduction

DNA glycosylases are a class of enzymes that function in base excision repair.  In base excision repair, DNA glycosylases break the bond between the damaged or incorrect base and the sugar of the nucleotide. The base is then flipped out of the helix and removed (Tywman 1998). DNA polymerase then fills in the missing base.  

 

DNA glycosylases are able to recognize multiple types of damaged bases, including deaminated cytosine and deaminated adenine.  Removal of these damaged bases appears to be vital to cell life, as no cell has yet to be discovered that does not contain DNA glycosylases (Moat et al 2002).

 

Properties of DNA glycosylases:

• They recognize a specific type of damaged base.
• The remove bases by breaking the N-glycosidic bond.
• They act only on single bases, not on larger lesions.
• A few act during mismatch repair. (Twyman 1998)

 

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Classifications

 

DNA glycosylases can be classified based on either their structure or function. 

Function: 

Monofunctional:  Monofunctional DNA glycosylases have only glycoslyase activities, meaning they only remove the damaged base. They require a separate endonuclease for the BER process to continue.(Moat et al 2002) 

 

Bifunctional:  Bifunctional DNA glycosylases have both glycosylase and endonuclease activities.  They are able to remove the base as well as nick a strand of the DNA backbone. (Moat et al 2002) 

 

Structure: 

DNA Glycosylases are grouped in structural superfamilies.  The current superfamilies are:  UDG, AAG, MutM/Fpg, and HhH-GPD. (Fromme et al Cur. Op. in Struct. Bio. 2004) 

 

The characteristic feature of the MutM/Fpg family is their use of a N-terminal praline residue as a nucleophile. The family was once believed to be found only in prokaryotes, but has now been identified in eukaryotes. (Frommet et al Cur. Op. in Struct. Bio. 2004)

 

The HhH-GPD family contain a helix-hairpin-helix structure which is followed by a glycine/proline rich region (Fromme et al Nature 2004).  This structure gives the family its name. 

 

The UDG family remove uracil from DNA.  The family has diverse functions and is found in both prokaryotes and eukaryotes. (Vallur et al 2005)

 

AAG stands for alkyladenine DNA glycosylase.  Members of the AAG family remove damaged purines. (Vallur et al 2005)

 

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Examples 

 

 

Human Uracil-DNA glycosylase:  

     Human Uracil-DNA glycosylase (UDG) removes uracil from DNA.  The activity of UDG is very specific.  It is able to differentiate between uracil and thymine and cytosine, which are very similar structurally (Kosaka et al 2007).

 

     The exact mechanism by which UDG works is not known. (Kosaka et al 2007)  Mol, et al (1995) suggest possible mechanisms.  They suggest that uracil is identified by interactions with the uracil at five points.  These interactions allow it to discriminate against cytosine.  The tight fit of uracil into the active site allows for discrimination against the larger thymine.  They also suggest that the His-268 region is directly involved in breaking the glycosylic bond (Mol et al 1995).  

 

 

Human UDG bound to DNA

 

 

OGG1: 

     OGG1 is a member of the HhH-GPD family (Fromme et al Cur. Op. in Struct. Bio. 2004).  OGG1 removes 8-oxoguanine (oxoG) and functions primarily in mammals (Hazra et al 2002).  Research suggests that OGG1 uses an intrahelical probe to locate the oxoG lesion(Banerjee et al 2006).  Banerjee, et al (2006) theorize that oxoG:C behave different than correct base pairings.  OGG1 flips the base out of the helix and into its active site (Banerjee et al 2006).

 

hOGG1 pathway from Current Biology (Cunningham 1997).                       G and oxoG complex image from Banerjee et al.

 

 

 

MutM: 

     MutM is the prokaryotic counterpart of OGG1.  While they are functionally similar, they are not structurally related. (Banerjee et al 2006)  MutM recognizes oxoG by using a projecting loop to contact the base.  Additional interactions between MutM and oxoG allow the enzyme to differentiate it from adenine, thymine, and cytosine.  It is able to identify the oxoG from guanine based on changes in the ring structure (Fromme & Verdine 2003).  As with OGG1, the base is flipped out from the DNA helix and inserted into an active site where the glycosylic bond is then broken (Banerjee et al 2006).

 

 

 

 

 

Endonuclease III:   

     Endonuclease III is a member of the HhH family.  It removes oxidized pyrimidines from DNA.  Endonuealse III contains a 4Fe-4S cluster.  Kuo, et al (1992) suggest that it is a representative for a new class of Fe-S glycosylases.  The Fe-S cluster is involved in DNA backbone recognition.  Endonuclease III contains a β-hairpin with thymine glycol recognition abilities which is involved in oxidized base recognition.(Kuo et al 1992)

Ribbon structure of Endonuclease III. The brown spheres (iron) and

the yellow spheres (sulfur) represent the Fe-S cluster. (Kuo et al 1992)

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Medical Importance

 

 

Huntington’s Disease: 

    Huntington’s disease is caused by CAG expansion on the Huntington’s disease gene (HD)^1-3.  The number of CAG repeats is positively correlated to disease severity.  High levels of oxidative damage are associated with increased CAG repeats.(Kovtun et al 2007)  Kvotun, et al. found that the loss of OGG1 significantly delayed expansion.  They theorized that OGG1 interacts with an already present CAG tract to expand the region.  Other glycosylases have not been found to be involved in this process.(Kovtun et al 2007)

 

Alzheimer’s Disease: 

     Oxidative damage has been implicated in the development of Alzheimer’s Disease (AD).  A build up of oxidative damages can result in cell death.  OGG1 initiates oxidative damage repair (Shao et al 2008).  In a study conducted by Shao, et al. (2008), it was found that OGG1 levels were low in both mild cognitive impairment subjects as well as Alzheimer’s subjects.   They suggested this finding indicates that low OGG1 levels, and thus oxidative damage buildup, play a role in early AD development.

 

Cancer: 

     Ongoing cancer research conducted by Guo, et al (2008) has found a link between the cancer gene, Ugene, and uracil-DNA Glycosylase.  Ugene is a gene commonly found over expressed in malignant colon cancers.  The gene has two transcripts, Ugene-p and Ugene-q. Guo et al found that Ugene-p binds to uracil DNA glycosylase 2 (UNG2).  They found that the binding of Ugene-p does not the affect the activity of UNG2 in vitro (Guo et al 2008).

     Inactivation of repair pathways are often targets for cancers.  Shoa et al suggest that the action of UNG2 is more complex in vivo, and Ugene-p may have an affect on damage repair in humans (Guo et al 2008).  Further research is needed to determine the effect of Ugene in vivo.

 

Hyper IgM Syndrome:

     Hyper IgM Syndrome (HIGM) is characterized by high levels of IgM antibodies.  This disorder causes an increased susceptibility to infection. Activation induced cytidine deaminase (AID) is required for normal immune function.  Patients with HIGM show deficiencies in AID.  Research by Imai et al suggests that UNG is vital for the workings of AID (Imai et al 2003).  Deficiencies in UDG thus contribute to HIGM.  The exact mechanism of this disorder is still not full understood, so further research into this disorder is necessary.

  

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References: 

 

Banerjee, A., Santos, W.L. & Verdine, G.L. Structure of a DNA Glycosylase searching for lesions. Science 311, 1153-1157 (2006)

 

Fromme, C.J., Banerjee, A., Huang, S.J. & Verdine, G.L. Structural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylase. Nature 427, 652-655 (2004)

 

Fromme, C.J., Banerjee A. & Verdine, G.L. DNA glycosylase recognition and catalysis. Current Opinion in Structural Biology 14, 43-49 (2004)

 

Fromme, C.J. & Verdine, G.L. DNA lesion recognition by the bacterial repair enzyme MutM. The Journal of Biological Chemistry 278, 51543-51548 (2003)

 

 

Guo, C., Zhang, X., Fink, S.P., Platzer, P., Wilson, K., Willson, J.K.V., Wang, Z. & Markowitz, S.D. Ugene, a newly identified protein that is commonly over-expressed in cancer, that binds uracil DNA glycosylase. Cancer Research 68, 6118-6126 (2008)

 

Hazra, T.K., Izumi, T., Boldogh, I., Imhoff, B., Kow, Y.W., Jaruga, P., Dizdaroglu, M. & Mitra, S. Identification and characterization of a human DNA glycosylase for repair of modified bases in oxidatively damaged DNA. Proceedings of the National Academy of Sciences 99, 3523-3528 (2002)

 

Imai, K., Slupphaug, G., Lee, W., Revy, P., Nonoyama, S., Catalan, N., Yel, L., Forveille, M., Kavli, B., Krokan, H., Ochs, H., Fischer, A., Durandy, A. Human uracil-DNA glycosylase deficiency associated with profoundly impaired immunoglobulin class-switch recombination. Nature Immunology 4, 1023-1028 (2003)

 

Kosaka, H., Hoseki, J., Nakagawa, N., Kuramitsu, S.& Masui, R. Crystal structure of family 5 uracil-DNA Glycosylase bound to DNA. Journal of Molecular Biology 373, 839-850 (2007)

 

Kovtun, I.K., Lui, Y., Bjoras, M., Klungland, A., Wilson, S.H. & McMurray, C.T. OGG1 initiates age-dependent CAG trinucleotide expansionin somatic cells. Nature 447,477-452 (2007)

 

Kuo, C., McRee, D.E., Fisher, C.L., O'Handley, S.F., Cunningham, R.P. & Tainer, J.A. Atomic structure of the DNA repair [4Fe-4S] enzyme endonuclease III. Science 258, 434-440 (1992)

 

Lin, J., Singh, R.R.P. & Cox, D.L. Theoretical study of DNA damage recognition via electron transfer from the [4Fe-4S] complex of MutY. Biophysical Journal 95, 3259-3268 (2008)

 

Moat, A.G., Foster, J.W., & Spector, M.P. 2002. Microbial Physiology. John Wiley and Sons, Inc. New York, New York, pg 158-159.

 

Mol, C.D., Arvai, A.S., Slupphaug, G., Kavli, B., Alseth, I., Krokan, H.E. & Tainer, J.A. Crystal structure and mutational analysis of human Uracil-DNA glycosylase:  structural basis for specificity and catalysis. Cell 80, 869-878 (1995)

 

Shao, C., Xiong, S., Li, G., Gu, L., Mao, G., Markesbery, W.R. & Lovell M.A. Altered 8-oxoguanine glycosylase in mild cognitive impairment and late-stage Alzheimer's disease brain. Free Radical Biology &  Medicine 45,813-819 (2008)

 

Twyman, R.M. 1998. Advanced Molecular Biology: A Concise Reference. BIOS Scientific Publishers, Ltd. Oxford, UK, p191

 

Vallur, A.C., Maher, R.L. & Bloom, L.B. The efficiency of hypoxanthine excision by alkyladenine DNA glycosylase is altered by changes in nearest neighbor bases. DNA Repair 4, 1088-1098 (2005)