XPD Helicase (3CRV)

XPD Helicase

Xeroderma pigmentosum group D (XPD) helicase is a subunit of Transcription Factor IIH (TFIIH), which aids in transcription initiation and DNA repair. XPD helicse unwinds DNA, allowing other DNA repair enzymes to access and correct damaged regions in the DNA. XPD helicase helps to fix DNA damaged by ultraviolet (UV) light radiation; therefore mutations in XPD helicase results in diseases characterized by light sensitivity.

Structure

XPD helicase's catalytic core (Figure 1) is composed of four domains, HD1 (green), HD2 (red), 4FeS (brown), and Arch (blue), and six motifs. The HD1 and HD2 domains form the ATP-Binding Interface.The 4FeS (pink) domain contains Cysteines 88, 102, 105, and 137 that bind the Sulfur-Iron cluster; this domain helps to detect DNA damage. Single stranded DNA (ssDNA) binding is facilitated by the 4FeS domain's Fe-S region, and a channel is formed with HD1 and Arch Domains to form a passage way for the ssDNA. Positively charged residues along the channel are paired with negatively charged residues to allow subsequent ssDNA binding and movement along the ssDNA. The HD2 and Arch domain form the HD2 gateway, which is associated with sensing bulky DNA damage as well. The motif's (Figure 2), I (31-60, red), II (177-186, blue), III (317-327, green), IV (394-408, brown), V (439-455, purple) and VI (501-517, orange), all play a role in both ATP and DNA binding. Motif's I, II, V, and VI all form the ATP binding site at the HD1 and HD2 interface (Figure 3). Motif's IV, V, and VI within the HD2 domain form the gateway channel for DNA binding (Figure 4)^[1]. (Reset Protein)

Function

XPD helicase is an essential subunit of the general transcription factor IIH (TFIIH), which is a complex that, along with other general transcription factors, helps to initiate transcription and repair damaged DNA ^[2]. XPD helicase helps to stabilize the structure of TFIIH but also plays a functional role in repairing DNA as a helicase enzyme ^[1]. Helicases are enzymes that unwind double-stranded DNA into single-stranded DNA so that other enzymes, like polymerases, can act upon the DNA ^[3]. In the context of DNA repair, helicases unwind DNA and other enzymes remove the damaged DNA and replace it with the complementary nucleotides based on the other DNA sequence. When DNA is exposed to UV radiation, adjacent nucleotide bases, often thymines, can react and form bulky pyrimidine dimers, which can block enzymes that work on DNA ^[4]. For example, during DNA replication, thymine dimers do not fit into the active site of DNA polymerases smoothly, sometimes resulting in mismatched nucleotides. To fix this type of damage on single strands of DNA, cells employ a process called nucleotide excision repair (NER) ^[1]. This is the type of DNA repair that TFIIH, with the help of the XPD helicase subunit, carries out to remove the damaged DNA.

Breaking the hydrogen bonds that hold the two DNA strands together requires energy, so XPD helicase is dependent on ATP ^[5]. The ATP-dependent helicase activity of XPD helicase, however is only required for NER, even though TFIIH participates in both repair and transcription initiation ^[6]. XPD helicase not only unravels the DNA around the damage, but also helps TFIIH in recognizing bulky lesions in DNA ^[7]. The DNA is then threaded through the central pore of XPD helicase, which then opens up the double helix.

Disease

The NER pathway consists of 28 genes, three of which are part of TFIIH, and mutations in many of these are associated with a set of diseases that are similar but have marked differences ^[8]. Mutations in XPD helicase are associated with three distinct diseases: Cockayne Syndrome (CS), Xeroderma Pigmentosum (XP), and trichothiodystrophy (TTD) ^[9]. The common symptom between these diseases is sensitivity to UV light because of defects in the repair system that fixes mutations caused by UV radiation ^[1]. CS is characterized by short stature, signs of premature aging, failure to gain weight, impaired development of the nervous system, and photosensitivity ^[10]. XP is characterized by extreme sensitivity to sunlight and a higher risk of skin cancer. Some XP patients have neurological degeneration, which can be explained by the fact that neurons do not divide, and mutations that are not corrected by NER could accumulate and eventually lead to cell death ^[8]. TTD is characterized by sparse and brittle hair, pregnancy-induced high blood pressure, intellectual disabilities, a higher risk of recurrent respiratory infections, and photosensitivity ^[11]. It has been proposed that specific mutations in XPD helicase affect the transcription activities of TFIIH more than its repair activities, resulting in development issues that lead to intellectual disabilities ^[8]. Interestingly, only XP has been found to be associated with an increased risk of skin cancer; studies are being conducted to determine why some mutations in XPD helicase result in a higher risk of skin cancer and others do not. Different types of mutations in XPD helicase as well as interactions between XPD helicase mutations and defects in other NER proteins can result in these different diseases. Due to the complexity of these interactions, little is known about the molecular basis for the differences in these diseases ^[8].

References

1. ↑ ^{1.0 1.1 1.2 1.3} Fan L, Fuss JO, Cheng QJ, Arvai AS, Hammel M, Roberts VA, Cooper PK, Tainer JA. XPD helicase structures and activities: insights into the cancer and aging phenotypes from XPD mutations. Cell. 2008 May 30;133(5):789-800. PMID:18510924 doi:10.1016/j.cell.2008.04.030
2. ↑ Mydlikova Z, Gursky J, Pirsel M. Transcription factor IIH - the protein complex with multiple functions. Neoplasma. 2010;57(4):287-90. PMID:20429618
3. ↑ Tuteja N, Tuteja R. Unraveling DNA helicases. Motif, structure, mechanism and function. Eur J Biochem. 2004 May;271(10):1849-63. PMID:15128295 doi:http://dx.doi.org/10.1111/j.1432-1033.2004.04094.x
4. ↑ Vink AA, Roza L. Biological consequences of cyclobutane pyrimidine dimers. J Photochem Photobiol B. 2001 Dec 31;65(2-3):101-4. PMID:11809365
5. ↑ Buechner CN, Heil K, Michels G, Carell T, Kisker C, Tessmer I. Strand-specific recognition of DNA damages by XPD provides insights into nucleotide excision repair substrate versatility. J Biol Chem. 2014 Feb 7;289(6):3613-24. doi: 10.1074/jbc.M113.523001. Epub 2013, Dec 14. PMID:24338567 doi:http://dx.doi.org/10.1074/jbc.M113.523001
6. ↑ Kuper J, Braun C, Elias A, Michels G, Sauer F, Schmitt DR, Poterszman A, Egly JM, Kisker C. In TFIIH, XPD helicase is exclusively devoted to DNA repair. PLoS Biol. 2014 Sep 30;12(9):e1001954. doi: 10.1371/journal.pbio.1001954., eCollection 2014 Sep. PMID:25268380 doi:http://dx.doi.org/10.1371/journal.pbio.1001954
7. ↑ Constantinescu-Aruxandei D, Petrovic-Stojanovska B, Penedo JC, White MF, Naismith JH. Mechanism of DNA loading by the DNA repair helicase XPD. Nucleic Acids Res. 2016 Feb 20. pii: gkw102. PMID:26896802 doi:http://dx.doi.org/10.1093/nar/gkw102
8. ↑ ^{8.0 8.1 8.2 8.3} Kraemer KH, Patronas NJ, Schiffmann R, Brooks BP, Tamura D, DiGiovanna JJ. Xeroderma pigmentosum, trichothiodystrophy and Cockayne syndrome: a complex genotype-phenotype relationship. Neuroscience. 2007 Apr 14;145(4):1388-96. Epub 2007 Feb 1. PMID:17276014 doi:http://dx.doi.org/10.1016/j.neuroscience.2006.12.020
9. ↑ Liu J, Fang H, Chi Z, Wu Z, Wei D, Mo D, Niu K, Balajee AS, Hei TK, Nie L, Zhao Y. XPD localizes in mitochondria and protects the mitochondrial genome from oxidative DNA damage. Nucleic Acids Res. 2015 Jun 23;43(11):5476-88. doi: 10.1093/nar/gkv472. Epub 2015, May 12. PMID:25969448 doi:http://dx.doi.org/10.1093/nar/gkv472
10. ↑ Nance MA, Berry SA. Cockayne syndrome: review of 140 cases. Am J Med Genet. 1992 Jan 1;42(1):68-84. PMID:1308368 doi:http://dx.doi.org/10.1002/ajmg.1320420115
11. ↑ Hashimoto S, Egly JM. Trichothiodystrophy view from the molecular basis of DNA repair/transcription factor TFIIH. Hum Mol Genet. 2009 Oct 15;18(R2):R224-30. doi: 10.1093/hmg/ddp390. PMID:19808800 doi:http://dx.doi.org/10.1093/hmg/ddp390