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PDBsum entry 2fz4
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DNA binding protein PDB id
2fz4

 

 

 

 

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Contents
Protein chain
206 a.a. *
Waters ×39
* Residue conservation analysis
PDB id:
2fz4
Name: DNA binding protein
Title: Crystal structure of the n-terminal half of archaeoglobus fulgidus xpb
Structure: DNA repair protein rad25. Chain: a. Fragment: n-terminal half. Engineered: yes
Source: Archaeoglobus fulgidus. Organism_taxid: 224325. Strain: dsm 4304. Gene: rad25. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.40Å     R-factor:   0.243     R-free:   0.265
Authors: L.Fan,J.A.Tainer
Key ref:
L.Fan et al. (2006). Conserved XPB core structure and motifs for DNA unwinding: implications for pathway selection of transcription or excision repair. Mol Cell, 22, 27-37. PubMed id: 16600867 DOI: 10.1016/j.molcel.2006.02.017
Date:
09-Feb-06     Release date:   18-Apr-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O29889  (O29889_ARCFU) -  DNA repair protein RAD25 from Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)
Seq:
Struc: 		452 a.a.
206 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1016/j.molcel.2006.02.017 Mol Cell 22:27-37 (2006)
PubMed id: 16600867  
 
 
Conserved XPB core structure and motifs for DNA unwinding: implications for pathway selection of transcription or excision repair.
L.Fan, A.S.Arvai, P.K.Cooper, S.Iwai, F.Hanaoka, J.A.Tainer.
 
  ABSTRACT  
 
The human xeroderma pigmentosum group B (XPB) helicase is essential for transcription, nucleotide excision repair, and TFIIH functional assembly. Here, we determined crystal structures of an Archaeoglobus fulgidus XPB homolog (AfXPB) that characterize two RecA-like XPB helicase domains and discover a DNA damage recognition domain (DRD), a unique RED motif, a flexible thumb motif (ThM), and implied conformational changes within a conserved functional core. RED motif mutations dramatically reduce helicase activity, and the DRD and ThM, which flank the RED motif, appear structurally as well as functionally analogous to the MutS mismatch recognition and DNA polymerase thumb domains. Substrate specificity is altered by DNA damage, such that AfXPB unwinds dsDNA with 3' extensions, but not blunt-ended dsDNA, unless it contains a lesion, as shown for CPD or (6-4) photoproducts. Together, these results provide an unexpected mechanism of DNA unwinding with implications for XPB damage verification in nucleotide excision repair.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Structural Comparison of XPB HD2 Insertion ThM with the Thumb Domain of T7 DNA Polymerase and Taq DNA Polymerase 		Figure 6.
Figure 6. Proposed Structure-Based Mechanism whereby Damage Verification by XPB Promotes Unwinding of Damaged dsDNA for NER
 
  The above figures are reprinted by permission from Cell Press: Mol Cell (2006, 22, 27-37) copyright 2006.  
  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.  
21132514 X.Ma, Y.Hong, W.Han, D.Sheng, J.Ni, G.Hou, and Y.Shen (2011).
Single-stranded DNA binding activity of XPBI, but not XPBII, from Sulfolobus tokodaii causes double-stranded DNA melting.
  Extremophiles, 15, 67-76.  
20606254 D.E.Kainov, V.Cura, M.Vitorino, H.Nierengarten, P.Poussin, B.Kieffer, J.Cavarelli, and A.Poterszman (2010).
Structure determination of the minimal complex between Tfb5 and Tfb2, two subunits of the yeast transcription/DNA-repair factor TFIIH: a retrospective study.
  Acta Crystallogr D Biol Crystallogr, 66, 745-755.  
19942596 I.Rybanská, J.Gursky, M.Fasková, E.P.Salazar, E.Kimlícková-Polakovicová, K.Kleibl, L.H.Thompson, and M.Pirsel (2010).
Newly identified CHO ERCC3/XPB mutations and phenotype characterization.
  Mutagenesis, 25, 179-185.  
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.  
21142660 R.Metzger, E.Bollschweiler, A.H.Hölscher, and U.Warnecke-Eberz (2010).
ERCC1: impact in multimodality treatment of upper gastrointestinal cancer.
  Future Oncol, 6, 1735-1749.  
19063897 D.S.Shin, M.Didonato, D.P.Barondeau, G.L.Hura, C.Hitomi, J.A.Berglund, E.D.Getzoff, S.C.Cary, and J.A.Tainer (2009).
Superoxide dismutase from the eukaryotic thermophile Alvinella pompejana: structures, stability, mechanism, and insights into amyotrophic lateral sclerosis.
  J Mol Biol, 385, 1534-1555.
PDB codes: 3f7k 3f7l
19759013 H.M.Roth, I.Tessmer, B.Van Houten, and C.Kisker (2009).
Bax1 is a novel endonuclease: implications for archaeal nucleotide excision repair.
  J Biol Chem, 284, 32272-32278.  
19625490 N.T.Uyen, S.Y.Park, J.W.Choi, H.J.Lee, K.Nishi, and J.S.Kim (2009).
The fragment structure of a putative HsdR subunit of a type I restriction enzyme from Vibrio vulnificus YJ016: implications for DNA restriction and translocation activity.
  Nucleic Acids Res, 37, 6960-6969.
PDB code: 3h1t
19145234 P.J.McKinnon (2009).
DNA repair deficiency and neurological disease.
  Nat Rev Neurosci, 10, 100-112.  
19713942 V.Oksenych, B.B.de Jesus, A.Zhovmer, J.M.Egly, and F.Coin (2009).
Molecular insights into the recruitment of TFIIH to sites of DNA damage.
  EMBO J, 28, 2971-2980.  
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.  
18205545 F.Altieri, C.Grillo, M.Maceroni, and S.Chichiarelli (2008).
DNA damage and repair: from molecular mechanisms to health implications.
  Antioxid Redox Signal, 10, 891-937.  
18332124 J.Banroques, O.Cordin, M.Doère, P.Linder, and N.K.Tanner (2008).
A conserved phenylalanine of motif IV in superfamily 2 helicases is required for cooperative, ATP-dependent binding of RNA substrates in DEAD-box proteins.
  Mol Cell Biol, 28, 3359-3371.  
18510924 L.Fan, J.O.Fuss, Q.J.Cheng, A.S.Arvai, M.Hammel, V.A.Roberts, P.K.Cooper, and J.A.Tainer (2008).
XPD helicase structures and activities: insights into the cancer and aging phenotypes from XPD mutations.
  Cell, 133, 789-800.
PDB codes: 3crv 3crw
18033706 O.D.Schärer (2008).
A molecular basis for damage recognition in eukaryotic nucleotide excision repair.
  Chembiochem, 9, 21-23.  
18029358 R.A.Pugh, M.Honda, H.Leesley, A.Thomas, Y.Lin, M.J.Nilges, I.K.Cann, and M.Spies (2008).
The iron-containing domain is essential in Rad3 helicases for coupling of ATP hydrolysis to DNA translocation and for targeting the helicase to the single-stranded DNA-double-stranded DNA junction.
  J Biol Chem, 283, 1732-1743.  
  18473724 R.Gupta, and R.M.Brosh (2008).
Helicases as prospective targets for anti-cancer therapy.
  Anticancer Agents Med Chem, 8, 390-401.  
17466626 F.Coin, V.Oksenych, and J.M.Egly (2007).
Distinct roles for the XPB/p52 and XPD/p44 subcomplexes of TFIIH in damaged DNA opening during nucleotide excision repair.
  Mol Cell, 26, 245-256.  
17174478 J.J.Perry, L.Fan, and J.A.Tainer (2007).
Developing master keys to brain pathology, cancer and aging from the structural biology of proteins controlling reactive oxygen species and DNA repair.
  Neuroscience, 145, 1280-1299.  
17962020 O.Maillard, U.Camenisch, F.C.Clement, K.B.Blagoev, and H.Naegeli (2007).
DNA repair triggered by sensors of helical dynamics.
  Trends Biochem Sci, 32, 494-499.  
17154534 C.G.Bunick, M.R.Miller, B.E.Fuller, E.Fanning, and W.J.Chazin (2006).
Biochemical and structural domain analysis of xeroderma pigmentosum complementation group C protein.
  Biochemistry, 45, 14965-14979.  
16819517 G.Miller, and S.Hahn (2006).
A DNA-tethered cleavage probe reveals the path for promoter DNA in the yeast preinitiation complex.
  Nat Struct Mol Biol, 13, 603-610.  
16752948 J.O.Fuss, and P.K.Cooper (2006).
DNA repair: dynamic defenders against cancer and aging.
  PLoS Biol, 4, e203.  
16947863 K.S.Oh, S.G.Khan, N.G.Jaspers, A.Raams, T.Ueda, A.Lehmann, P.S.Friedmann, S.Emmert, A.Gratchev, K.Lachlan, A.Lucassan, C.C.Baker, and K.H.Kraemer (2006).
Phenotypic heterogeneity in the XPB DNA helicase gene (ERCC3): xeroderma pigmentosum without and with Cockayne syndrome.
  Hum Mutat, 27, 1092-1103.  
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 codes are shown on the right.

 

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