Click here to close
Hello! We notice that you are using Internet Explorer, which is not supported by Xenbase and may cause the site to display incorrectly.
We suggest using a current version of Chrome,
FireFox, or Safari.
Protein Sci
2001 Mar 01;103:560-71. doi: 10.1110/ps.29401.
Show Gene links
Show Anatomy links
Identification of intrinsic order and disorder in the DNA repair protein XPA.
Iakoucheva LM
,
Kimzey AL
,
Masselon CD
,
Bruce JE
,
Garner EC
,
Brown CJ
,
Dunker AK
,
Smith RD
,
Ackerman EJ
.
???displayArticle.abstract???
The DNA-repair protein XPA is required to recognize a wide variety of bulky lesions during nucleotide excision repair. Independent NMR solution structures of a human XPA fragment comprising approximately 40% of the full-length protein, the minimal DNA-binding domain, revealed that one-third of this molecule was disordered. To better characterize structural features of full-length XPA, we performed time-resolved trypsin proteolysis on active recombinant Xenopus XPA (xXPA). The resulting proteolytic fragments were analyzed by electrospray ionization interface coupled to a Fourier transform ion cyclotron resonance mass spectrometry and SDS-PAGE. The molecular weight of the full-length xXPA determined by mass spectrometry (30922.02 daltons) was consistent with that calculated from the sequence (30922.45 daltons). Moreover, the mass spectrometric data allowed the assignment of multiple xXPA fragments not resolvable by SDS-PAGE. The neural network program Predictor of Natural Disordered Regions (PONDR) applied to xXPA predicted extended disordered N- and C-terminal regions with an ordered internal core. This prediction agreed with our partial proteolysis results, thereby indicating that disorder in XPA shares sequence features with other well-characterized intrinsically unstructured proteins. Trypsin cleavages at 30 of the possible 48 sites were detected and no cleavage was observed in an internal region (Q85-I179) despite 14 possible cut sites. For the full-length xXPA, there was strong agreement among PONDR, partial proteolysis data, and the NMR structure for the corresponding XPA fragment.
Ackerman,
Nucleotide excision repair in oocyte nuclear extracts from Xenopus laevis.
2000, Pubmed,
Xenbase
Ackerman,
Nucleotide excision repair in oocyte nuclear extracts from Xenopus laevis.
2000,
Pubmed
,
Xenbase
Araújo,
Protein complexes in nucleotide excision repair.
1999,
Pubmed
Aviles,
The conformation of histone H5. Isolation and characterisation of the globular segment.
1978,
Pubmed
Bode,
The transition of bovine trypsinogen to a trypsin-like state upon strong ligand binding. The refined crystal structures of the bovine trypsinogen-pancreatic trypsin inhibitor complex and of its ternary complex with Ile-Val at 1.9 A resolution.
1978,
Pubmed
Bothner,
Evidence of viral capsid dynamics using limited proteolysis and mass spectrometry.
1998,
Pubmed
Bruce,
High-mass-measurement accuracy and 100% sequence coverage of enzymatically digested bovine serum albumin from an ESI-FTICR mass spectrum.
1999,
Pubmed
Buchko,
Interactions of human nucleotide excision repair protein XPA with DNA and RPA70 Delta C327: chemical shift mapping and 15N NMR relaxation studies.
1999,
Pubmed
Buchko,
Extended X-ray absorption fine structure evidence for a single metal binding domain in Xenopus laevis nucleotide excision repair protein XPA.
1999,
Pubmed
,
Xenbase
Buchko,
Structural features of the minimal DNA binding domain (M98-F219) of human nucleotide excision repair protein XPA.
1998,
Pubmed
Chou,
Empirical predictions of protein conformation.
1978,
Pubmed
Cohen,
Probing the solution structure of the DNA-binding protein Max by a combination of proteolysis and mass spectrometry.
1995,
Pubmed
Daughdrill,
The C-terminal half of the anti-sigma factor, FlgM, becomes structured when bound to its target, sigma 28.
1997,
Pubmed
Dolgikh,
Alpha-Lactalbumin: compact state with fluctuating tertiary structure?
1981,
Pubmed
Dunker,
Protein disorder and the evolution of molecular recognition: theory, predictions and observations.
1998,
Pubmed
Fletcher,
4E binding proteins inhibit the translation factor eIF4E without folded structure.
1998,
Pubmed
Fontana,
Correlation between sites of limited proteolysis and segmental mobility in thermolysin.
1986,
Pubmed
Gervasoni,
Identification of the binding surface on beta-lactamase for GroEL by limited proteolysis and MALDI-mass spectrometry.
1998,
Pubmed
Horn,
Automated reduction and interpretation of high resolution electrospray mass spectra of large molecules.
2000,
Pubmed
Hubbard,
Modeling studies of the change in conformation required for cleavage of limited proteolytic sites.
1994,
Pubmed
Hubbard,
Assessment of conformational parameters as predictors of limited proteolytic sites in native protein structures.
1998,
Pubmed
Huber,
Conformational flexibility in protein molecules.
1979,
Pubmed
Ikegami,
Solution structure of the DNA- and RPA-binding domain of the human repair factor XPA.
1998,
Pubmed
Kissinger,
Crystal structures of human calcineurin and the human FKBP12-FK506-calcineurin complex.
1995,
Pubmed
Kuraoka,
Identification of a damaged-DNA binding domain of the XPA protein.
1996,
Pubmed
Laemmli,
Cleavage of structural proteins during the assembly of the head of bacteriophage T4.
1970,
Pubmed
Li,
Predicting Protein Disorder for N-, C-, and Internal Regions.
1999,
Pubmed
Manalan,
Activation of calcineurin by limited proteolysis.
1983,
Pubmed
Massotte,
Structure of the membrane-bound form of the pore-forming domain of colicin A: a partial proteolysis and mass spectrometry study.
1993,
Pubmed
Miyamoto,
Mutational analysis of the structure and function of the xeroderma pigmentosum group A complementing protein. Identification of essential domains for nuclear localization and DNA excision repair.
1992,
Pubmed
Nigg,
Nucleocytoplasmic transport: signals, mechanisms and regulation.
1997,
Pubmed
Oda,
DNA polymerases alpha and beta are required for DNA repair in an efficient nuclear extract from Xenopus oocytes.
1996,
Pubmed
,
Xenbase
Ohgushi,
'Molten-globule state': a compact form of globular proteins with mobile side-chains.
1983,
Pubmed
Riek,
NMR structure of the mouse prion protein domain PrP(121-231).
1996,
Pubmed
Romero,
Sequence complexity of disordered protein.
2001,
Pubmed
Rost,
Combining evolutionary information and neural networks to predict protein secondary structure.
1994,
Pubmed
Schweers,
Structural studies of tau protein and Alzheimer paired helical filaments show no evidence for beta-structure.
1994,
Pubmed
Senko,
Automated assignment of charge states from resolved isotopic peaks for multiply charged ions.
1995,
Pubmed
Shimamoto,
Molecular cloning of human XPAC gene homologs from chicken, Xenopus laevis and Drosophila melanogaster.
1991,
Pubmed
,
Xenbase
Solovyev,
Predicting alpha-helix and beta-strand segments of globular proteins.
1994,
Pubmed
Sugasawa,
Xeroderma pigmentosum group C protein complex is the initiator of global genome nucleotide excision repair.
1998,
Pubmed
Wakasugi,
Order of assembly of human DNA repair excision nuclease.
1999,
Pubmed
Weinreb,
NACP, a protein implicated in Alzheimer's disease and learning, is natively unfolded.
1996,
Pubmed
Williams,
The protein non-folding problem: amino acid determinants of intrinsic order and disorder.
2001,
Pubmed
Wright,
Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm.
1999,
Pubmed
