PDBsum entry 2qsh

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protein dna_rna Protein-protein interface(s) links
DNA binding protein/DNA PDB id
Protein chains
502 a.a. *
54 a.a. *
* Residue conservation analysis
PDB id:
Name: DNA binding protein/DNA
Title: Crystal structure of rad4-rad23 bound to a mismatch DNA
Structure: DNA repair protein rad4. Chain: a. Synonym: rad4. Engineered: yes. Uv excision repair protein rad23. Chain: x. Synonym: rad23. Engineered: yes. Top strand of the mismatch DNA.
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: rad4. Expressed in: trichoplusia ni. Expression_system_taxid: 7111. Expression_system_cell_line: hi5. Expression_system_organ: eggs. Gene: rad23.
2.81Å     R-factor:   0.211     R-free:   0.244
Authors: J.-H.Min,N.P.Pavletich
Key ref:
J.H.Min and N.P.Pavletich (2007). Recognition of DNA damage by the Rad4 nucleotide excision repair protein. Nature, 449, 570-575. PubMed id: 17882165 DOI: 10.1038/nature06155
31-Jul-07     Release date:   02-Oct-07    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P14736  (RAD4_YEAST) -  DNA repair protein RAD4
754 a.a.
502 a.a.*
Protein chain
Pfam   ArchSchema ?
P32628  (RAD23_YEAST) -  UV excision repair protein RAD23
398 a.a.
54 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   1 term 
  Biological process     nucleotide-excision repair   2 terms 
  Biochemical function     DNA binding     2 terms  


DOI no: 10.1038/nature06155 Nature 449:570-575 (2007)
PubMed id: 17882165  
Recognition of DNA damage by the Rad4 nucleotide excision repair protein.
J.H.Min, N.P.Pavletich.
Mutations in the nucleotide excision repair (NER) pathway can cause the xeroderma pigmentosum skin cancer predisposition syndrome. NER lesions are limited to one DNA strand, but otherwise they are chemically and structurally diverse, being caused by a wide variety of genotoxic chemicals and ultraviolet radiation. The xeroderma pigmentosum C (XPC) protein has a central role in initiating global-genome NER by recognizing the lesion and recruiting downstream factors. Here we present the crystal structure of the yeast XPC orthologue Rad4 bound to DNA containing a cyclobutane pyrimidine dimer (CPD) lesion. The structure shows that Rad4 inserts a beta-hairpin through the DNA duplex, causing the two damaged base pairs to flip out of the double helix. The expelled nucleotides of the undamaged strand are recognized by Rad4, whereas the two CPD-linked nucleotides become disordered. These findings indicate that the lesions recognized by Rad4/XPC thermodynamically destabilize the Watson-Crick double helix in a manner that facilitates the flipping-out of two base pairs.
  Selected figure(s)  
Figure 3.
Figure 3: Rad4 binds to damaged DNA in two parts. a, TGD–BHD1 binds to an 11-bp segment of undamaged dsDNA, making extensive contacts to the DNA phosphate and ribose groups. Close-up view of the TGD–DNA interface, in an orientation similar to Fig. 1a, showing side-chain and backbone groups that contact the DNA. Green dotted lines indicate hydrogen bonds. b, Close-up view of the BHD1–dsDNA interface, in an orientation slightly rotated about the DNA axis relative to a. c, Schematic representation of the interactions shown in a and b. Van der Waals contacts to DNA, orange arrows; polar contacts between side chains and DNA, green arrows; and hydrogen bonds between backbone amide and DNA phosphate groups, blue arrows. d, BHD2–BHD3 bind to a 4-bp DNA segment that contains the CPD lesion. Close-up view of the interface in a similar orientation as in Fig. 1a, showing side chains that contact the DNA. The flipped-out thymidines of the undamaged strand are coloured black, and the disordered, CPD-linked thymidines are indicated schematically. e, Schematic representation of the interactions shown in d. Contacts are marked with arrows, as described in c.
Figure 4.
Figure 4: Rad4 undergoes conformational changes on DNA-binding. a, The Rad4–Rad23–DNA complex (red) is superimposed on the apo-Rad4–Rad23 complex (green) by aligning the TGDs. Black arrows indicate the movement of BHD1, BHD2 and BHD3 towards the DNA in the DNA-bound structure relative to the apo-Rad4–Rad23 structure. The BHD3 tip in the apo-Rad4–Rad23 structure is disordered and is not shown. The Rad23 R4BD is omitted for clarity. b, Model of undamaged B-type dsDNA bound to Rad4 showing that the apo-Rad4 but not the DNA-bound Rad4 conformation would allow binding to undamaged dsDNA. The model was prepared by superimposing a B-type dsDNA on the undamaged dsDNA portion of the Rad4–Rad23–DNA structure.
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2007, 449, 570-575) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22572993 E.Compe, and J.M.Egly (2012).
TFIIH: when transcription met DNA repair.
  Nat Rev Mol Cell Biol, 13, 343-354.  
20861000 M.Firczuk, M.Wojciechowski, H.Czapinska, and M.Bochtler (2011).
DNA intercalation without flipping in the specific ThaI-DNA complex.
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PDB code: 3ndh
21240268 M.Jaciuk, E.Nowak, K.Skowronek, A.Tańska, and M.Nowotny (2011).
Structure of UvrA nucleotide excision repair protein in complex with modified DNA.
  Nat Struct Mol Biol, 18, 191-197.
PDB code: 3pih
20730555 A.Guainazzi, and O.D.Schärer (2010).
Using synthetic DNA interstrand crosslinks to elucidate repair pathways and identify new therapeutic targets for cancer chemotherapy.
  Cell Mol Life Sci, 67, 3683-3697.  
20577208 C.Biertümpfel, Y.Zhao, Y.Kondo, S.Ramón-Maiques, M.Gregory, J.Y.Lee, C.Masutani, A.R.Lehmann, F.Hanaoka, and W.Yang (2010).
Structure and mechanism of human DNA polymerase eta.
  Nature, 465, 1044-1048.
PDB codes: 3mr2 3mr3 3mr4 3mr5 3mr6 3si8
20927102 E.H.Rubinson, A.S.Gowda, T.E.Spratt, B.Gold, and B.F.Eichman (2010).
An unprecedented nucleic acid capture mechanism for excision of DNA damage.
  Nature, 468, 406-411.
PDB codes: 3jx7 3jxy 3jxz 3jy1
19961237 F.Liang, and B.P.Cho (2010).
Enthalpy-entropy contribution to carcinogen-induced DNA conformational heterogeneity.
  Biochemistry, 49, 259-266.  
20502938 J.L.Tubbs, and J.A.Tainer (2010).
Alkyltransferase-like proteins: molecular switches between DNA repair pathways.
  Cell Mol Life Sci, 67, 3749-3762.  
19933257 J.Rudolf, C.Rouillon, U.Schwarz-Linek, and M.F.White (2010).
The helicase XPD unwinds bubble structures and is not stalled by DNA lesions removed by the nucleotide excision repair pathway.
  Nucleic Acids Res, 38, 931-941.  
19892827 K.L.Brown, M.Roginskaya, Y.Zou, A.Altamirano, A.K.Basu, and M.P.Stone (2010).
Binding of the human nucleotide excision repair proteins XPA and XPC/HR23B to the 5R-thymine glycol lesion and structure of the cis-(5R,6S) thymine glycol epimer in the 5'-GTgG-3' sequence: destabilization of two base pairs at the lesion site.
  Nucleic Acids Res, 38, 428-440.
PDB codes: 2kh5 2kh6
21117171 K.L.Jones, L.Zhang, K.L.Seldeen, and F.Gong (2010).
Detection of bulky DNA lesions: DDB2 at the interface of chromatin and DNA repair in eukaryotes.
  IUBMB Life, 62, 803-811.  
20439997 M.S.Luijsterburg, G.von Bornstaedt, A.M.Gourdin, A.Z.Politi, M.J.Moné, D.O.Warmerdam, J.Goedhart, W.Vermeulen, R.van Driel, and T.Höfer (2010).
Stochastic and reversible assembly of a multiprotein DNA repair complex ensures accurate target site recognition and efficient repair.
  J Cell Biol, 189, 445-463.  
20876134 N.Mathieu, N.Kaczmarek, and H.Naegeli (2010).
Strand- and site-specific DNA lesion demarcation by the xeroderma pigmentosum group D helicase.
  Proc Natl Acad Sci U S A, 107, 17545-17550.  
20039786 P.A.Muniandy, J.Liu, A.Majumdar, S.T.Liu, and M.M.Seidman (2010).
DNA interstrand crosslink repair in mammalian cells: step by step.
  Crit Rev Biochem Mol Biol, 45, 23-49.  
20007604 S.Malik, P.Chaurasia, S.Lahudkar, G.Durairaj, A.Shukla, and S.R.Bhaumik (2010).
Rad26p, a transcription-coupled repair factor, is recruited to the site of DNA lesion in an elongating RNA polymerase II-dependent manner in vivo.
  Nucleic Acids Res, 38, 1461-1477.  
20028083 T.M.Neher, N.I.Rechkunova, O.I.Lavrik, and J.J.Turchi (2010).
Photo-cross-linking of XPC-Rad23B to cisplatin-damaged DNA reveals contacts with both strands of the DNA duplex and spans the DNA adduct.
  Biochemistry, 49, 669-678.  
  20871811 Y.Cai, D.J.Patel, S.Broyde, and N.E.Geacintov (2010).
Base sequence context effects on nucleotide excision repair.
  J Nucleic Acids, 2010, 0.  
20855601 Y.Jiang, X.Wang, S.Bao, R.Guo, D.G.Johnson, X.Shen, and L.Li (2010).
INO80 chromatin remodeling complex promotes the removal of UV lesions by the nucleotide excision repair pathway.
  Proc Natl Acad Sci U S A, 107, 17274-17279.  
  20798892 Y.Shimizu, Y.Uchimura, N.Dohmae, H.Saitoh, F.Hanaoka, and K.Sugasawa (2010).
Stimulation of DNA Glycosylase Activities by XPC Protein Complex: Roles of Protein-Protein Interactions.
  J Nucleic Acids, 2010, 0.  
  19077538 H.Hashimoto, J.R.Horton, X.Zhang, and X.Cheng (2009).
UHRF1, a modular multi-domain protein, regulates replication-coupled crosstalk between DNA methylation and histone modifications.
  Epigenetics, 4, 8.
PDB codes: 3f8i 3f8j 3fde
19809470 J.E.Cleaver, E.T.Lam, and I.Revet (2009).
Disorders of nucleotide excision repair: the genetic and molecular basis of heterogeneity.
  Nat Rev Genet, 10, 756-768.  
19516334 J.L.Tubbs, V.Latypov, S.Kanugula, A.Butt, M.Melikishvili, R.Kraehenbuehl, O.Fleck, A.Marriott, A.J.Watson, B.Verbeek, G.McGown, M.Thorncroft, M.F.Santibanez-Koref, C.Millington, A.S.Arvai, M.D.Kroeger, L.A.Peterson, D.M.Williams, M.G.Fried, G.P.Margison, A.E.Pegg, and J.A.Tainer (2009).
Flipping of alkylated DNA damage bridges base and nucleotide excision repair.
  Nature, 459, 808-813.
PDB codes: 3gva 3gx4 3gyh
19162041 K.Kropachev, M.Kolbanovskii, Y.Cai, F.Rodríguez, A.Kolbanovskii, Y.Liu, L.Zhang, S.Amin, D.Patel, S.Broyde, and N.E.Geacintov (2009).
The sequence dependence of human nucleotide excision repair efficiencies of benzo[a]pyrene-derived DNA lesions: insights into the structural factors that favor dual incisions.
  J Mol Biol, 386, 1193-1203.  
19279666 L.Staresincic, A.F.Fagbemi, J.H.Enzlin, A.M.Gourdin, N.Wijgers, I.Dunand-Sauthier, G.Giglia-Mari, S.G.Clarkson, W.Vermeulen, and O.D.Schärer (2009).
Coordination of dual incision and repair synthesis in human nucleotide excision repair.
  EMBO J, 28, 1111-1120.  
19190661 O.D.Schärer, and A.J.Campbell (2009).
Wedging out DNA damage.
  Nat Struct Mol Biol, 16, 102-104.  
19684342 P.A.Muniandy, D.Thapa, A.K.Thazhathveetil, S.T.Liu, and M.M.Seidman (2009).
Repair of laser-localized DNA interstrand cross-links in G1 phase mammalian cells.
  J Biol Chem, 284, 27908-27917.  
19145234 P.J.McKinnon (2009).
DNA repair deficiency and neurological disease.
  Nat Rev Neurosci, 10, 100-112.  
19325626 S.Bergink, and S.Jentsch (2009).
Principles of ubiquitin and SUMO modifications in DNA repair.
  Nature, 458, 461-467.  
19200715 S.Schneider, S.Schorr, and T.Carell (2009).
Crystal structure analysis of DNA lesion repair and tolerance mechanisms.
  Curr Opin Struct Biol, 19, 87-95.  
19609301 U.Camenisch, D.Träutlein, F.C.Clement, J.Fei, A.Leitenstorfer, E.Ferrando-May, and H.Naegeli (2009).
Two-stage dynamic DNA quality check by xeroderma pigmentosum group C protein.
  EMBO J, 28, 2387-2399.  
18948114 Y.Cai, D.J.Patel, N.E.Geacintov, and S.Broyde (2009).
Differential nucleotide excision repair susceptibility of bulky DNA adducts in different sequence contexts: hierarchies of recognition signals.
  J Mol Biol, 385, 30-44.  
19109893 A.Scrima, R.Konícková, B.K.Czyzewski, Y.Kawasaki, P.D.Jeffrey, R.Groisman, Y.Nakatani, S.Iwai, N.P.Pavletich, and N.H.Thomä (2008).
Structural basis of UV DNA-damage recognition by the DDB1-DDB2 complex.
  Cell, 135, 1213-1223.
PDB codes: 3ei1 3ei2 3ei3 3ei4
18809580 B.M.Bernardes de Jesus, M.Bjørås, F.Coin, and J.M.Egly (2008).
Dissection of the molecular defects caused by pathogenic mutations in the DNA repair factor XPC.
  Mol Cell Biol, 28, 7225-7235.  
19014481 C.Dinant, A.B.Houtsmuller, and W.Vermeulen (2008).
Chromatin structure and DNA damage repair.
  Epigenetics Chromatin, 1, 9.  
18343204 D.L.Croteau, Y.Peng, and B.Van Houten (2008).
DNA repair gets physical: mapping an XPA-binding site on ERCC1.
  DNA Repair (Amst), 7, 819-826.  
19109889 G.Chu, and W.Yang (2008).
Here comes the sun: recognition of UV-damaged DNA.
  Cell, 135, 1172-1174.  
18772888 H.Hashimoto, J.R.Horton, X.Zhang, M.Bostick, S.E.Jacobsen, and X.Cheng (2008).
The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix.
  Nature, 455, 826-829.
PDB codes: 2zo0 2zo1 2zo2
18702509 M.B.Smeaton, E.M.Hlavin, T.McGregor Mason, A.M.Noronha, C.J.Wilds, and P.S.Miller (2008).
Distortion-dependent unhooking of interstrand cross-links in mammalian cell extracts.
  Biochemistry, 47, 9920-9930.  
18936173 M.Tremblay, Y.Teng, M.Paquette, R.Waters, and A.Conconi (2008).
Complementary roles of yeast Rad4p and Rad34p in nucleotide excision repair of active and inactive rRNA gene chromatin.
  Mol Cell Biol, 28, 7504-7513.  
18033706 O.D.Schärer (2008).
A molecular basis for damage recognition in eukaryotic nucleotide excision repair.
  Chembiochem, 9, 21-23.  
18166981 S.C.Shuck, E.A.Short, and J.J.Turchi (2008).
Eukaryotic nucleotide excision repair: from understanding mechanisms to influencing biology.
  Cell Res, 18, 64-72.  
18717677 S.Jacobelli, N.Soufir, J.J.Lacapere, S.Regnier, A.Bourillon, B.Grandchamp, G.Hétet, D.Pham, A.Palangie, M.F.Avril, N.Dupin, A.Sarasin, and I.Gorin (2008).
Xeroderma pigmentosum group C in a French Caucasian patient with multiple melanoma and unusual long-term survival.
  Br J Dermatol, 159, 968-973.  
18157156 W.Yang (2008).
Structure and mechanism for DNA lesion recognition.
  Cell Res, 18, 184-197.  
18574675 Y.Roche, D.Zhang, G.M.Segers-Nolten, W.Vermeulen, C.Wyman, K.Sugasawa, J.Hoeijmakers, and C.Otto (2008).
Fluorescence correlation spectroscopy of the binding of nucleotide excision repair protein XPC-hHr23B with DNA substrates.
  J Fluoresc, 18, 987-995.  
18774935 Y.S.Krasikova, N.I.Rechkunova, E.A.Maltseva, I.O.Petruseva, V.N.Silnikov, T.S.Zatsepin, T.S.Oretskaya, O.D.Schärer, and O.I.Lavrik (2008).
Interaction of nucleotide excision repair factors XPC-HR23B, XPA, and RPA with damaged DNA.
  Biochemistry (Mosc), 73, 886-896.  
18658245 Z.Bukowy, J.A.Harrigan, D.A.Ramsden, B.Tudek, V.A.Bohr, and T.Stevnsner (2008).
WRN Exonuclease activity is blocked by specific oxidatively induced base lesions positioned in either DNA strand.
  Nucleic Acids Res, 36, 4975-4987.  
17964258 O.D.Schärer (2007).
Achieving broad substrate specificity in damage recognition by binding accessible nondamaged DNA.
  Mol Cell, 28, 184-186.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.