Báo cáo khoa học: The protein shuffle Sequential interactions among components of the human nucleotide excision repair pathway pdf

MINIREVIEW The protein shuffle Sequential interactions among components of the human nucleotide excision repair pathway Chin-Ju Park and Byong-Seok Choi Department of Chemistry, National Creative Initiative Center, Korea Advanced Institute of Science and Technology, Guseong-dong, Yuseong-gu, Daejon, Korea In mammalian cells, nucleotide excision repair (NER) is the major DNA repair pathway for the removal of bulky adducts induced by UV light or other environ- mental carcinogens [1–3]. NER proteins display both versatility and specificity in that they (a) recognize various types of DNA damage and (b) discriminate between these lesions and the abundant undamaged DNA present in the genome (including the intact DNA strand opposite the lesion). Depending on the precise location of the damaged DNA, the NER pro- cess is referred to as either transcription-coupled repair (TCR) or global genomic repair (GGR). The TCR process specifically repairs blemishes on the transcribed DNA strands of active genes, while GGR eliminates lesions from the entire genome. As defects in NER are known to cause inherited diseases, such as xeroderma pigmentosum (XP), it is crucial that researchers deci- pher the mechanisms of NER at the molecular level. XP proteins A–G (i.e. XPA, XPB, XPC, XPD, XPE, XPF and XPG) are known to participate in various Keywords damage recognition; dual incision; nucleotide excision repair; protein–protein interaction; replication protein A; structure; xeroderma pigmentosa Correspondence B S. Choi, Department of Chemistry, National Creative Initiative Center, Korea Advanced Institute of Science and Technology (KAIST), 373–1 Guseong-dong, Yuseong-gu, Daejon 305–701, Korea Fax: +82 42 8692810 Tel: +82 42 8692868 E-mail: byongseok.choi@kaist.ac.kr (Received 12 December 2005, accepted 16 February 2006) doi:10.1111/j.1742-4658.2006.05189.x Xeroderma pigmentosum (XP) is an inherited disease in which cells from patients exhibit defects in nucleotide excision repair (NER). XP proteins A–G are crucial in the processes of DNA damage recognition and incision, and patients with XP can carry mutations in any of the genes that specify these proteins. In mammalian cells, NER is a dynamic process in which a variety of proteins interact with one another, via modular domains, to carry out their functions. XP proteins are key players in several steps of the NER process, including DNA strand discrimination (XPA, in complex with replication protein A), repair complex formation (XPC, in complex with hHR23B; XPF, in complex with ERCC1) and repair factor recruit- ment (transcription factor IIH, in complex with XPG). Through these pro- tein–protein interactions, various types of bulky DNA adducts can be recognized and repaired. Communication between the NER system and other cellular pathways is also achieved by selected binding of the various structural domains. Here, we summarize recent studies on the domain structures of human NER components and the regulatory networks that utilize these proteins. Data provided by these studies have helped to illu- minate the complex molecular interactions among NER factors in the con- text of DNA repair. Abbreviations CPD, cyclopyrimidine dimer; GGR, global genomic repair; (HhH) 2 , helix–hairpin–helix domain; MBD, minimal DNA-binding domain; NER, nucleotide excision repair; PH, pleckstrin homology; PTB, phosphotyrosine binding; RPA, replication protein A; TCR, transcription-coupled repair; TFIIH, transcription factor IIH; Ub, ubiquitin; UBA, ubiquitin association; UV-DDB, UV-damaged DNA-binding protein; XP, xeroderma pigmentosum. 1600 FEBS Journal 273 (2006) 1600–1608 ª 2006 The Authors Journal compilation ª 2006 FEBS aspects of DNA damage recognition and incision, and patients with XP can carry mutations in any of the genes that specify these proteins. Cell lines established from patients with mutations in one of these genes are referred to as XP-A, XP-B, XP-C, XP-D, XP-E, XP-F, or XP-G cells, depending on which gene houses the mutations. These cell lines have served as essential tools in studies of NER. Results from a wide variety of biochemical and bio- physical studies have illuminated mechanistic aspects of DNA damage recognition and incision in eukaryotic cells, and are reviewed herein. We will mainly discuss human NER in this review. These studies reveal that NER is a dynamic process in which pivotal proteins are assembled and disassembled as needed [4,5]. NER reactions: an overview The NER mechanism in mammalian cells involves (a) DNA damage recognition and assembly of the protein complex that carries out DNA incision around the lesion, (b) incision of the damaged DNA strand on both sides of the injury, which results in damage exci- sion, and (c) synthesis and ligation of a stretch of DNA to repair the gap created by the excision. In TCR, stalled RNA polymerase II acts as a marker for recognition of the lesion by the DNA repair machin- ery. With respect to the GGR pathway, although the order of arrival and departure of each factor at a lesion remains controversial, it is widely accepted that GGR in human cells occurs as follows. DNA damage- induced helical distortion is recognized by the XPC– hHR23B complex, and transcription factor IIH (TFIIH; which consists of nine subunits), XPA (a possible homodimer) and replication protein A (RPA, which consists of three subunits) arrive sequentially at the site of the damage and constitute the pre-incision complex. Endonuclease XPG and the XPF–ERCC1 complex are responsible for the 3¢ and 5¢ DNA inci- sions, respectively. Binding of XPG induces the release of XPC–hHR23B, whereas XPF–ERCC1 triggers exci- sion of the damaged DNA and the release of XPA and TFIIH. Subsequently, the newly formed gap in the DNA is filled by DNA polymerase d ⁄ e, replication factor C, proliferating cell nuclear antigen, RPA and DNA ligase I (Fig. 1). For the NER process to be executed successfully, multiple protein–protein and protein–DNA interac- tions must occur in the appropriate order. For exam- ple, XPC interacts with the p62 subunit of TFIIH and, in turn, p62 interacts with XPG. The results of intri- cate studies designed to characterize these interactions are reviewed below. The XPC–hHR23B complex: a sensor of helical distortion XPC and its partners XPC is a 125 kDa protein that interacts with a variety of factors, including hHR23B, TFIIH and DNA. XPC is known to form a stable complex with the hHR23B and centrin2 proteins (see below). Although the XPC subunit is solely responsible for binding of the XPC– hHR23B complex to sites of DNA damage, hHR23B stimulates XPC to function in NER and is also necessary for XPA–RPA-mediated displacement of the Fig. 1. Scheme of the global genomic repair (GGR) pathway. The sequential arrivals and departures of nucleotide excision repair (NER) components are marked with arrows. Proteins are defined throughout the text. Adapted by permission from Macmillan Pub- lishers Ltd: EMBO Journal, [4], copyright (2003). C J. Park & B S. Choi The protein shuffle in NER pathway FEBS Journal 273 (2006) 1600–1608 ª 2006 The Authors Journal compilation ª 2006 FEBS 1601 XPC–hHR23B complex from damaged DNA during the early stages of the NER process [5] (Fig. 2A). hHR23B is a 58 kDa human homolog of the yeast NER protein, RAD23. In addition to an XPC-binding domain, hHR23B has an N-terminal ubiquitin (Ub)- like domain and two Ub-association domains (UBA1 and UBA2). Therefore, hHR23B is a modular protein, and solution structures of its domains and possible intramolecular binding surfaces have been described [6] (Fig. 2B,C). Recently, the centrin 2 protein, which exists in a complex with XPC and hHR23B, was shown to stimulate the NER activity of XPC by enhancing damage recognition [7]. A recent report revealed that, upon UV irradiation, XPC undergoes reversible ubiquitylation, and this reaction depends on the presence of a UV-damaged DNA-binding protein (UV-DDB). The UV-DDB com- plex consists of the DDB1 (p127) and DDB2 (p48) proteins. When UV irradiates cells, it is associated with Cullin 4A, Roc1 and Cop9 signalosome, which are components of ubiquitin ligase (E3) [8]. The UV-DDB binds specifically to lesions caused by UV irradiation, such as (6–4) photoproducts and cyclopyrimidine dimers (CPDs). Studies of XP-E cells, which have mutations in the DDB2 gene, have revealed that the UV-DDB represents an initial damage sensor, especi- ally for CPD lesions. However, the mechanism by which UV-DDB and XPC are functionally linked, in terms of damage recognition, in the GGR process remains to be elucidated. Sugasawa et al. showed that the ubiquitylation of XPC is involved in the transfer of the UV-induced DNA lesion from UV-DDB to XPC. Even though UV-induced multi-ubiquitylation of XPC occurs through the UV-DDB-associated E3 complex, it does not serve as a signal for protein degradation. The UBA domains of hHR23B are thought to protect XPC from the ubiquitin ⁄ proteasome system. XPC is also modified by SUMO-1 – a member of the small ubiqu- itin-like modifier family of proteins – following UV irradiation, and this modification event is dependent on XPA activity [9], which is known to be necessary for preventing UV-induced XPC degradation. There- fore, sumoylation is believed to play a role in stabiliza- tion of the XPC protein. These various UV-induced post-transcriptional modifications of XPC appear to be crucial for the serial binding and release of proteins to and from the DNA-damage site, before and after XPC binding. However, the precise molecular interac- tions that orchestrate this intricate game of musical chairs are not yet fully understood (Fig. 2C). The 3D structures of the core XPC-binding domains of hHR23B and hHR23A have been solved [10,11] (Fig. 2C). These two XPC-binding domains each con- sist of five similar alpha helices, as well as differentially distributed hydrophobic surfaces that make direct con- tact with the XPC. The DNA-binding domain of XPC overlaps with its hHR23B interaction domain [12]. However, a dearth of structural information for the hHR23B-binding site of XPC makes it difficult to determine precisely how these proteins interact with each other. A B C Fig. 2. Structures of the nucleotide excision repair (NER) players. (A) Domain structure of the human xeroderma pigmentosum C (XPC) protein. Binding sites for interaction partners are shown with arrows. (B) Domain structure of the hHR23B protein. (C) Solution structures for each domain of hHR23B. UbL, ubiquitin-like domain. The Protein Data Bank (PDB) entry code for Ubl is 1P1A. UBA, ubiquitin association domain. UBA1 and UBA2 structures were derived for hHR23; the PDB entry codes are 1IFY and 1 DV0, respectively. The PDB entry code for the XPC-binding domain of hHR23B is 1PVE. All figures were generated from PDB files using SWISS-PDB VIEWER and POV-RAY. The linker regions, which were not structurally determined, are shown by dotted lines. Important bind- ing partners are also indicated as connecting arrows. Ubiquitin interacts with UBA1 and UBA2, as well as PubS2, in the protea- some complex. UbL can bind with the same partners, UBA1, UBA2 and PubS2. The XPC-binding domain binds to XPC. The protein shuffle in NER pathway C J. Park & B S. Choi 1602 FEBS Journal 273 (2006) 1600–1608 ª 2006 The Authors Journal compilation ª 2006 FEBS The XPC–hHR23B complex is known to interact preferentially with damaged DNA substrates, such as (6–4) photoproducts or acetaminoflorene adducts [1,13,14]. However, XPC-hHR23B recognizes CPDs poorly, which implies that recognition of such lesions requires additional factors [15]. By using a series of artificial DNA substrates that contained mismatched bases opposite a CPD, Sugasawa et al. performed a series of experiments, the results of which suggest that the increased structural distortion caused by having a mismatched base opposite a CPD enhances XPC– hHR23B binding to these lesions [15]. This hypothesis was supported by the results of an NMR structural study of DNA decamers that was designed to elucidate the influence of mismatched bases on the DNA struc- tures containing CPD [16]. Although the hydrogen bonds between CPDs and the mismatched bases are maintained, helical bending, backbone conformation and the major and ⁄ or minor grooves differ between CPDs that have correct bases and CPDs that have mismatched bases on the opposite DNA strand. There- fore, these structural properties might play a role in determining the binding affinity of XPC–hHR23B for DNA. Furthermore, it is known that DNA bending is induced by UV-DDB binding to damaged DNA sites. Taken together, these findings suggest that the struc- tural properties of DNA-damaged substrates, whether intrinsic or the result of protein binding, function in the recruitment of the XPC–hHR23B complex to sites of DNA damage. The protein shuffle In the GGR pathway, one study has shown that XPC–hHR23B interacts with the p62 subunit of TFIIH and recruits TFIIH to sites of helical distort- ion [17]. Another study has suggested that XPC– hHR23B is able to interact with XPA during the transition from an initial damage-recognition inter- mediate (involving XPC and TFIIH) to the forma- tion of an ultimate incision complex [5]. In NER assays reconstituted in vitro , XPC does not remain in contact with the DNA substrate during the dual incision reaction, as this initial damage sensor is released from the excision machine when XPG and XPA associate with the damaged DNA [4,5,18]. It is still not known how hHR23B triggers XPC displace- ment from damaged DNA upon arrival of the XPA– RPA complex or which domains of XPC and XPA are responsible for interacting each other. More research is required to elucidate the various steps of this handing-off process that occurs in the initial steps of NER. TFIIH: shuttling between repair and transcription TFIIH consists of nine protein subunits: XPB, XPD, p62, p52, p44, p34, cdk7, cyclin H and MAT1. XPB and XPD are DNA helicases, and their ATP-depend- ent DNA unwinding activities have been reviewed pre- viously [19]. In addition to its helicase activities, TFIIH is directly responsible for the recruitment of XPG and XPA to the nascent DNA damage excision complex [20,21]. A recent NMR study revealed that the N-terminal region of the p62 subunit of TFIIH contains a pleckstrin homology ⁄ phosphotyrosine bind- ing (PH ⁄ PTB) domain that associates with XPG [22]. The PH ⁄ PTB domain adopts a b-sandwich fold that (a) contains two nearly orthogonal b-sheets made up of seven antiparallel b-strands and (b) is closed off at one end by a long C-terminal a-helix (Fig. 3). Because this domain also interacts with acidic transcriptional activator proteins, such as p53 and VP16, the involve- ment of the PH domain in NER raises interesting questions regarding the dual role of TFIIH in tran- scription and DNA repair. It is known that TFIIH complexes which have been released from the NER dual-incision complex can support mRNA synthesis by RNA polymerase II in a reconstituted transcription assay. Moreover, it was shown recently that yeast TFIIH houses a Ub ligase (E3) activity that plays a regulatory role in the transcription of DNA damage response genes. Specifically, the RING finger motifs in Fig. 3. Transcription factor IIH (TFIIH). (A) Molecular composition of TFIIH and its interacting partners. (B) Solution structure of the N-terminal region of the p62 subunit. The PDB entry code is 1PFJ. C J. Park & B S. Choi The protein shuffle in NER pathway FEBS Journal 273 (2006) 1600–1608 ª 2006 The Authors Journal compilation ª 2006 FEBS 1603 the Ssl1 subunit of yeast TFIIH are responsible for the observed Ub ligase activity [23] (Ssl is a homolog of the p44 subunit of human TFIIH). This finding sug- gests that TFIIH participates in DNA repair, not only through its commonly required helicase activities, but also through the transcriptional regulation of DNA repair genes. XPA-RPA: a linchpin of the NER network of interactions XPA is a 36 kDa zinc metalloprotein that interacts with many other NER subunits, such as RPA (see below), ERCC1 (a binding partner of XPF, a 5¢ endo- nuclease) and TFIIH (see above) [21,24,25]. The N-ter- minal region of XPA (residues 1–97) is responsible for the interaction with RPA32 and ERCC1. The central part of the protein (residues 98–219) consists of zinc finger and loop-rich subdomains, which are able to bind to RPA70 and DNA [24,26] (Fig. 4). The NMR structure of this domain showed the existence of a pos- itively charged cleft and confirmed that DNA binding occurs in the loop-rich subdomain and that RPA70 interactions occur in the zinc-binding core [27]. NMR studies also showed that the ERCC1-binding region of XPA is unstructured and forms a transient intramole- cular association with the DNA-binding domain of XPA [28]. These results suggest that ERCC1 binding to XPA would be possible only after damaged DNA displaces the XPA ERCC1-binding region from its DNA-binding domain. RPA is an abundant, heterotrimeric ssDNA-binding complex that is composed of 70-, 32- and 14 kDa polypeptide subunits (RPA70, RPA32 and RPA14). The ssDNA-binding activity resides mainly in the cen- tral region of the 70 kDa subunit, which contains two tandem oligonucleotide binding folds [29–31]. The oligonucleotide binding folds consist of five b strands coiled to form a closed b barrel that is capped by an a helix located between the third and fourth b strands. ssDNA binds to the protein via extensive electrostatic interactions and stacking contacts. The rest of RPA70, as well as its DNA-binding domain, interact with protein partners that are involved in DNA repair, recombination and replication pathways (Fig. 4) [32–36]. In the NER system, RPA participates in both early and late steps of the process. For example, early in the NER process, RPA assists TFIIH in the opening of the DNA helix around the damage site [36]. Further- more, in the presence of the XPA minimal DNA- binding domain (XPA-MBD), RPA70AB (residues 181–422) shows a tendency to interact with the undam- aged strand opposite the DNA damage site [32]. This result implies that RPA protects the intact DNA strand from inadvertent nuclease attack. With respect to XPA–RPA interactions, NMR analysis of RPA70 (residues 1–326) and XPA–MBD (residues 98–219) fragments revealed that the XPA-MBD site of RPA overlaps with its ssDNA-binding region. Therefore, XPA–RPA interactions appear to be modulated by ssDNA–RPA binding [34]. RPA32 (residues 172–270) also interacts with the N-terminal region of XPA in a manner similar to the mode of RPA32 binding to human uracil-DNA glycosylase and Rad52. This result reveals that RPA participates in multiple DNA repair Fig. 4. Domain structure of the human xeroderma pigmentosum A (XPA) protein and solution structure of the XPA minimal DNA-binding domain (XPA–MBD) (PDB entry: 1XPA). 3D structures of each domain in the human replication protein A (RPA) protein are shown. These include the C-terminal part of RPA32 (PDB entry: 1DPU), the N-terminal part of RPA70 (PDB entry: 1EWI), the RPA70AB–dC8 complex (PDB entry: 1JMC), and the trimerization core, which consists of the C-terminal part of RPA70, the N-terminal part of RPA32, and the N-terminal part of RPA14 (PDB entry: 1LIO). The protein shuffle in NER pathway C J. Park & B S. Choi 1604 FEBS Journal 273 (2006) 1600–1608 ª 2006 The Authors Journal compilation ª 2006 FEBS pathways by selective binding to functionally distinct partner proteins [37]. In later steps of the NER pathway, the XPA–RPA complex interacts with XPG and the XPF–ERCC1 com- plex. Through a stable interaction with TFIIH, XPG is already present in the NER complex prior to the arrival of the XPA subunit [20]. The interaction between XPA– RPA and XPG contributes to their association with the DNA substrate mutually [4]. RPA remains in NER complexes after the dual incision reactions and partici- pates in the DNA resynthesis step (Fig. 1). XPG and the XPF–ERCC1 complex: structure-specific nucleases XPG is a 133 kDa protein and a member of the FEN-1 family of structure-specific nucleases. As is the case with other members of the FEN-1 family, XPG has two highly conserved nuclease motifs known as the N- and I regions [38]. Although these regions are sep- arated by only a short helical loop in other FEN-1 family members, the N- and I regions in XPG are separated by a large insertion that was shown to be responsible for the binding of XPG to the other TFIIH subunits [39]. In addition to mediating pro- tein–protein interactions, the spacer region may also contribute to the substrate specificity of XPG. These findings demonstrate that XPG acts as a modular pro- tein, helping to orchestrate progression through the NER process via its functionally independent domains which interact specifically with other NER proteins and DNA substrates [39]. XPF–ERCC1 is the last protein complex to join the NER incision complex, and it does so by interacting specifically with both XPA and RPA [40]. XPG is also required for the recruitment of XPF–ERCC1 to the site of DNA damage and accomplishes this task by inducing a structural change in the pre-incision com- plex. XPF–ERCC1 cleaves DNA at sites 5¢ to the lesion. The XPF subunit consists of three domains, namely (a) an N-terminal helicase-like domain, (b) a central nuclease domain, and (c) a C-terminal helix– hairpin–helix [(HhH) 2 ] domain; the ERCC1 subunit consists of only two domains, namely (a) a central region that is similar to the XPF nuclease domain, but is devoid of residues characteristic of proteins with nuclease activity, and (b) a C-terminal (HhH) 2 domain (Fig. 5). The C-terminal (HhH) 2 domains of both XPF and ERCC1 mediate binding between the two proteins, mainly by hydrophobic interactions [41]. Recently, a crystal structure of the crenarchaeal XPF homodimer, alone and bound to double-stran- ded DNA (dsDNA) [42], the central domain of human ERCC1 as well as the (HhH) 2 domain het- erodimer of human XPF–ERCC1 [43], and a solu- tion structure of human XPF–ERCC1 (HhH) 2 domain complex [44], were published (Fig. 5). The central domain of human ERCC1 closely resembles the nuclease domains of XPF from humans and other organisms, despite low percentages of sequence identity. Investigations into DNA interaction of the protein complex have provided an insight into the roles of ERCC1 in the NER process. Tsodikov and his Fig. 5. Domain structures of the human xeroderma pigmentosum F (XPF) and ERCC1 proteins. Crystal structure of a complex containing the C-terminal domains of human XPF and ERCC1 (PDB entry: 2A1J) (left); crystal structure of the central domain of human ERCC1 (PDB entry: 2A1I) (right). C J. Park & B S. Choi The protein shuffle in NER pathway FEBS Journal 273 (2006) 1600–1608 ª 2006 The Authors Journal compilation ª 2006 FEBS 1605 collaborators reported that positively charged and aro- matic residues in the central domain of ERCC1 are spe- cially responsible for its interaction with ssDNA [43]. It was also observed that the each component of the XPF–ERCC1 (HhH) 2 complex displayed the ability to bind to ssDNA in their crystal structure. Chemical shift perturbation data of Tripsianes and his collaborators is not fully consistent with the previous model. They indi- cated that the (HhH) 2 domain of ERCC1 has the DNA-binding activity that is not possessed by (HhH) 2 domain of XPF [44]. Even though there is an inconsis- tency which remains to be identified, these results show that ERCC1 serves to localize the XPF nuclease domain properly by binding the ssDNA strand through the central and (HhH) 2 domains [45]. Conclusion and perspectives Recent studies have emphasized that components of the NER process interact with one another in a dynamic manner and participate in other DNA meta- bolizing pathways using their diverse structural domains. The structural studies described above were instrumental in deciphering the details of the various molecular interactions among NER players, such as those that occur in the XPC–hHR23B, XPA–RPA and XPF–ERCC1 complexes. The observations, that hHR23B contains Ub-relat- ed modules and that XPC undergoes ubiquitylation, raise the possibility that the protein degradation pro- teasome pathway can communicate with the NER pathway. Another intriguing finding is that a number of the NER proteins are multifunctional. For exam- ple, TFIIH plays a critical role in both RNA poly- merase II transcription and the DNA repair process by interacting with suitable protein partners. Mul- tiple roles for RPA have also been documented. For example, RPA functions in NER as well as other DNA processing reactions by selective binding to a variety of proteins. Results from the collection of studies described in this article highlight several important questions that need to be answered if researchers are to fully define the NER process. To achieve this, scientists will need to produce a detailed map of the sequential protein assembly processes that occur during damage recogni- tion and repair. Acknowledgements This work was supported by the National Creative Research Initiative Program to B S.C. from the Minis- try of Science and Technology, Korea. References 1 Batty DP & Wood RD (2000) Damage recognition in nucleotide excision repair of DNA. Gene 241, 193– 204. 2 de Laat WL, Jaspers NG & Hoeijmakers JH (1999) Molecular mechanism of nucleotide excision repair. Genes Dev 13, 768–785. 3 Wood RD (1999) DNA damage recognition during nuc- leotide excision repair in mammalian cells. Biochimie 81, 39–44. 4 Riedl T, Hanaoka F & Egly JM (2003) The comings and goings of nucleotide excision repair factors on damaged DNA. EMBO J 22, 5293–5303. 5 You JS, Wang M & Lee SH (2003) Biochemical analysis of the damage recognition process in nucleotide excision repair. J Biol Chem 278, 7476–7485. 6 Ryu KS, Lee KJ, Bae SH, Kim BK, Kim KA & Choi BS (2003) Binding surface mapping of intra- and inter- domain interactions among hHR23B, ubiquitin, and polyubiquitin binding site 2 of S5a. J Biol Chem 278, 36621–36627. 7 Nishi R, Okuda Y, Watanabe E, Mori T, Iwai S, Masu- tani C, Sugasawa K & Hanaoka F (2005) Centrin 2 sti- mulates nucleotide excision repair by interacting with xeroderma pigmentosum group C protein. Mol Cell Biol 25, 5664–5674. 8 Sugasawa K, Okuda Y, Saijo M, Nishi R, Matsuda N, Chu G, Mori T, Iwai S, Tanaka K & Hanaoka F (2005) UV-induced ubiquitylation of XPC protein mediated by UV-DDB-ubiquitin ligase complex. Cell 121, 387–400. 9 Wang QE, Zhu Q, Wani G, El-Mahdy MA, Li J & Wani AA (2005) DNA repair factor XPC is modified by SUMO-1 and ubiquitin following UV irradiation. Nucleic Acids Res 33, 4023–4034. 10 Kim B, Ryu KS, Kim HJ, Cho SJ & Choi BS (2005) Solution structure and backbone dynamics of the XPC- binding domain of the human DNA repair protein hHR23B. Febs J 272, 2467–2476. 11 Kamionka M & Feigon J (2004) Structure of the XPC binding domain of hHR23A reveals hydrophobic patches for protein interaction. Protein Sci 13, 2370– 2377. 12 Uchida A, Sugasawa K, Masutani C, Dohmae N, Araki M, Yokoi M, Ohkuma Y & Hanaoka F (2002) The carboxy-terminal domain of the XPC protein plays a crucial role in nucleotide excision repair through inter- actions with transcription factor IIH. DNA Repair (Amst) 1, 449–461. 13 Kusumoto R, Masutani C, Sugasawa K, Iwai S, Araki M, Uchida A, Mizukoshi T & Hanaoka F (2001) Diver- sity of the damage recognition step in the global geno- mic nucleotide excision repair in vitro. Mutat Res 485, 219–227. The protein shuffle in NER pathway C J. Park & B S. Choi 1606 FEBS Journal 273 (2006) 1600–1608 ª 2006 The Authors Journal compilation ª 2006 FEBS 14 Sugasawa K, Ng JM, Masutani C, Iwai S, van der Spek PJ, Eker AP, Hanaoka F, Bootsma D & Hoeijmakers JH (1998) Xeroderma pigmentosum group C protein complex is the initiator of global genome nucleotide excision repair. Mol Cell 2, 223–232. 15 Sugasawa K, Okamoto T, Shimizu Y, Masutani C, Iwai S & Hanaoka F (2001) A multistep damage recognition mechanism for global genomic nucleotide excision repair. Genes Dev 15, 507–521. 16 Lee JH, Park CJ, Shin JS, Ikegami T, Akutsu H & Choi BS (2004) NMR structure of the DNA decamer duplex containing double T*G mismatches of cis-syn cyclobu- tane pyrimidine dimer: implications for DNA damage recognition by the XPC-hHR23B complex. Nucleic Acids Res 32, 2474–2481. 17 Yokoi M, Masutani C, Maekawa T, Sugasawa K, Ohkuma Y & Hanaoka F (2000) The xeroderma pigmentosum group C protein complex XPC-HR23B plays an important role in the recruitment of transcrip- tion factor IIH to damaged DNA. J Biol Chem 275, 9870–9875. 18 Wakasugi M & Sancar A (1998) Assembly, subunit composition, and footprint of human DNA repair exci- sion nuclease. Proc Natl Acad Sci USA 95, 6669–6674. 19 Dip R, Camenisch U & Naegeli H (2004) Mechanisms of DNA damage recognition and strand discrimination in human nucleotide excision repair. DNA Repair (Amst) 3, 1409–1423. 20 Araujo SJ, Nigg EA & Wood RD (2001) Strong func- tional interactions of TFIIH with XPC and XPG in human DNA nucleotide excision repair, without a pre- assembled repairosome. Mol Cell Biol 21, 2281–2291. 21 Park CH, Mu D, Reardon JT & Sancar A (1995) The general transcription-repair factor TFIIH is recruited to the excision repair complex by the XPA protein inde- pendent of the TFIIE transcription factor. J Biol Chem 270, 4896–4902. 22 Gervais V, Lamour V, Jawhari A, Frindel F, Wasielew- ski E, Dubaele S, Egly JM, Thierry JC, Kieffer B & Poterszman A (2004) TFIIH contains a PH domain involved in DNA nucleotide excision repair. Nat Struct Mol Biol 11, 616–622. 23 Takagi Y, Masuda CA, Chang WH, Komori H, Wang D, Hunter T, Joazeiro CA & Kornberg RD (2005) Ubiquitin ligase activity of TFIIH and the transcriptional response to DNA damage. Mol Cell 18, 237–243. 24 Li L, Lu X, Peterson CA & Legerski RJ (1995) An interaction between the DNA repair factor XPA and replication protein A appears essential for nucleotide excision repair. Mol Cell Biol 15 , 5396–5402. 25 Park CH & Sancar A (1994) Formation of a ternary complex by human XPA, ERCC1, and ERCC4 (XPF) excision repair proteins. Proc Natl Acad Sci USA 91, 5017–5021. 26 Kuraoka I, Morita EH, Saijo M, Matsuda T, Morikawa K, Shirakawa M & Tanaka K (1996) Identification of a damaged-DNA binding domain of the XPA protein. Mutat Res 362, 87–95. 27 Ikegami T, Kuraoka I, Saijo M, Kodo N, Kyogoku Y, Morikawa K, Tanaka K & Shirakawa M (1998) Solu- tion structure of the DNA- and RPA-binding domain of the human repair factor XPA. Nat Struct Biol 5, 701–706. 28 Buchko GW, Isern NG, Spicer LD & Kennedy MA (2001) Human nucleotide excision repair protein XPA: NMR spectroscopic studies of an XPA fragment contain- ing the ERCC1-binding region and the minimal DNA- binding domain (M59–F219). Mutat Res 486, 1–10. 29 Bochkareva E, Belegu V, Korolev S & Bochkarev A (2001) Structure of the major single-stranded DNA- binding domain of replication protein A suggests a dynamic mechanism for DNA binding. EMBO J 20, 612–618. 30 Bochkarev A, Pfuetzner RA, Edwards AM & Frappier L (1997) Structure of the single-stranded-DNA-binding domain of replication protein A bound to DNA. Nature 385, 176–181. 31 Gomes XV & Wold MS (1996) Functional domains of the 70-kilodalton subunit of human replication protein A. Biochemistry 35, 10558–10568. 32 Lee JH, Park CJ, Arunkumar AI, Chazin WJ & Choi BS (2003) NMR study on the interaction between RPA and DNA decamer containing cis-syn cyclobutane pyrimidine dimer in the presence of XPA: implication for damage verification and strand-specific dual incision in nucleotide excision repair. Nucleic Acids Res 31, 4747–4754. 33 Stauffer ME & Chazin WJ (2004) Physical interaction between replication protein A and Rad51 promotes exchange on single-stranded DNA. J Biol Chem 279, 25638–25645. 34 Daughdrill GW, Buchko GW, Botuyan MV, Arrow- smith C, Wold MS, Kennedy MA & Lowry DF (2003) Chemical shift changes provide evidence for overlapping single-stranded DNA- and XPA-binding sites on the 70 kDa subunit of human replication protein A. Nucleic Acids Res 31, 4176–4183. 35 Arunkumar AI, Klimovich V, Jiang X, Ott RD, Mizoue L, Fanning E & Chazin WJ (2005) Insights into hRPA32 C-terminal domain-mediated assembly of the simian virus 40 replisome. Nat Struct Mol Biol 12, 332–339. 36 Evans E, Moggs JG, Hwang JR, Egly JM & Wood RD (1997) Mechanism of open complex and dual incision formation by human nucleotide excision repair factors. EMBO J 16, 6559–6573. 37 Mer G, Bochkarev A, Gupta R, Bochkareva E, Frappier L, Ingles CJ, Edwards AM & Chazin WJ (2000) Struc- tural basis for the recognition of DNA repair proteins UNG2, XPA, and RAD52 by replication factor RPA. Cell 103, 449–456. C J. Park & B S. Choi The protein shuffle in NER pathway FEBS Journal 273 (2006) 1600–1608 ª 2006 The Authors Journal compilation ª 2006 FEBS 1607 38 Lieber MR (1997) The FEN-1 family of structure-speci- fic nucleases in eukaryotic DNA replication, recombina- tion and repair. Bioessays 19, 233–240. 39 Dunand-Sauthier I, Hohl M, Thorel F, Jaquier-Gubler P, Clarkson SG & Scharer OD (2005) The spacer region of XPG mediates recruitment to nucleotide excision repair complexes and determines substrate specificity. J Biol Chem 280, 7030–7037. 40 Volker M, Mone MJ, Karmakar P, van Hoffen A, Schul W, Vermeulen W, Hoeijmakers JH, van Driel R, van Zeeland AA & Mullenders LH (2001) Sequential assembly of the nucleotide excision repair factors in vivo. Mol Cell 8, 213–224. 41 Choi YJ, Ryu KS, Ko YM, Chae YK, Pelton JG, Wemmer DE & Choi BS (2005) Biophysical characteri- zation of the interaction domains and mapping of the contact residues in the XPF-ERCC1 complex. J Biol Chem 280, 28644–28652. 42 Newman M, Murray-Rust J, Lally J, Rudolf J, Fadden A, Knowles PP, White MF & McDonald NQ (2005) Structure of an XPF endonuclease with and without DNA suggests a model for substrate recognition. EMBO J 24, 895–905. 43 Tsodikov OV, Enzlin JH, Scharer OD & Ellenberger T (2005) Crystal structure and DNA binding functions of ERCC1, a subunit of the DNA structure-specific endo- nuclease XPF-ERCC1. Proc Natl Acad Sci USA 102, 11236–11241. 44 Tripsianes K, Folkers G, Ab E, Das D, Odijk H, Jas- pers NG, Hoeijmakers JH, Kaptein R & Boelens R (2005) The structure of the human ERCC1 ⁄ XPF inter- action domains reveals a complementary role for the two proteins in nucleotide excision repair. Structure 13, 1849–1858. 45 Bunick CG & Chazin WJ (2005) Two blades of the [ex]scissor. Structure 13, 1740–1741. The protein shuffle in NER pathway C J. Park & B S. Choi 1608 FEBS Journal 273 (2006) 1600–1608 ª 2006 The Authors Journal compilation ª 2006 FEBS . MINIREVIEW The protein shuffle Sequential interactions among components of the human nucleotide excision repair pathway Chin-Ju Park and Byong-Seok. displacement of the Fig. 1. Scheme of the global genomic repair (GGR) pathway. The sequential arrivals and departures of nucleotide excision repair (NER) components