[NMR paper] NMR structure of the human Rad18 zinc finger in complex with ubiquitin defines a class of UBZ domains in proteins linked to the DNA damage response.
NMR structure of the human Rad18 zinc finger in complex with ubiquitin defines a class of UBZ domains in proteins linked to the DNA damage response.
Biochemistry. 2014 Aug 27;
Authors: Rizzo AA, Salerno PE, Bezsonova I, Korzhnev DM
Abstract
Ubiquitin-mediated interactions are critical for the cellular DNA damage response (DDR). Therefore, many DDR-related proteins contain ubiquitin-binding domains, including ubiquitin-binding zinc fingers (UBZs). The majority of these UBZ domains belong to the C2H2 (type 3 Pol?-like) or C2HC (type 4 Rad18-like) families. We have used NMR spectroscopy to characterize the binding to ubiquitin and determine the structure of the type 4 UBZ domain (UBZ4) from human Rad18, which is a key ubiquitin ligase in the DNA damage tolerance pathway responsible for mono-ubiquitination of the DNA sliding clamp PCNA. The Rad18-UBZ domain binds ubiquitin with micromolar affinity and adopts a ?1-?2-? fold similar to the previously characterized type 3 UBZ domain (UBZ3) from the translesion synthesis DNA polymerase Pol?. However, despite nearly identical structures, a disparity in the location of binding-induced NMR chemical shift perturbations shows that the Rad18-UBZ4 and Pol?-UBZ3 bind ubiquitin in distinctly different modes. The Rad18-UBZ4 interacts with ubiquitin with the ?-helix and the ?1-strand as shown by the structure of the Rad18-UBZ - ubiquitin complex determined in this work, while the Pol?-UBZ3 exclusively utilizes the ?-helix. Our findings suggest the existence of two classes of UBZ domains in DDR-related proteins with similar structures but unique ubiquitin binding properties and provide context for further study to establish the differential roles of these domains in the complex cellular response to DNA damage.
PMID: 25162118 [PubMed - as supplied by publisher]
[NMR paper] Solution structure of an archaeal DNA binding protein with an eukaryotic zinc finger fold.
Solution structure of an archaeal DNA binding protein with an eukaryotic zinc finger fold.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.plosone.org-images-pone_120x30.png http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Solution structure of an archaeal DNA binding protein with an eukaryotic zinc finger fold.
PLoS One. 2013;8(1):e52908
Authors: Guillière F, Danioux C, Jaubert C, Desnoues N, Delepierre M, Prangishvili D, Sezonov G, Guijarro JI
...
nmrlearner
Journal club
0
02-03-2013 10:19 AM
Pb-207 NMR Spectroscopy Reveals that Pb(II) Coordinates with Glutathione (GSH) and Tris Cysteine Zinc Finger Proteins in a PbS(3) Coordination Environment.
Pb-207 NMR Spectroscopy Reveals that Pb(II) Coordinates with Glutathione (GSH) and Tris Cysteine Zinc Finger Proteins in a PbS(3) Coordination Environment.
Pb-207 NMR Spectroscopy Reveals that Pb(II) Coordinates with Glutathione (GSH) and Tris Cysteine Zinc Finger Proteins in a PbS(3) Coordination Environment.
J Inorg Biochem. 2011 Aug 1;105(8):1030-1034
Authors: Neupane KP, Pecoraro VL
(207)Pb NMR spectroscopy can be used to monitor the binding of Pb(II) to thiol rich biological small molecules such as glutathione and to zinc finger proteins. The...
nmrlearner
Journal club
0
06-01-2011 02:30 PM
[NMR paper] NMR structure of the single QALGGH zinc finger domain from the Arabidopsis thaliana S
NMR structure of the single QALGGH zinc finger domain from the Arabidopsis thaliana SUPERMAN protein.
Related Articles NMR structure of the single QALGGH zinc finger domain from the Arabidopsis thaliana SUPERMAN protein.
Chembiochem. 2003 Mar 3;4(2-3):171-80
Authors: Isernia C, Bucci E, Leone M, Zaccaro L, Di Lello P, Digilio G, Esposito S, Saviano M, Di Blasio B, Pedone C, Pedone PV, Fattorusso R
Zinc finger domains of the classical type represent the most abundant DNA binding domains in eukaryotic transcription factors. Plant proteins...
nmrlearner
Journal club
0
11-24-2010 09:01 PM
[NMR paper] NMR and molecular dynamics studies of the hydration of a zinc finger-DNA complex.
NMR and molecular dynamics studies of the hydration of a zinc finger-DNA complex.
Related Articles NMR and molecular dynamics studies of the hydration of a zinc finger-DNA complex.
J Mol Biol. 2000 Oct 6;302(5):1101-17
Authors: Tsui V, Radhakrishnan I, Wright PE, Case DA
The hydration of a high-affinity protein-DNA complex involving the three amino terminal zinc finger domains of transcription factor IIIA (TFIIIA) and a 15-base-pair DNA duplex was investigated by NMR spectroscopy and molecular dynamics (MD) simulations. Intermolecular nuclear...
nmrlearner
Journal club
0
11-19-2010 08:29 PM
[NMR paper] NMR structure of the complex between the zinc finger protein NCp10 of Moloney murine
NMR structure of the complex between the zinc finger protein NCp10 of Moloney murine leukemia virus and the single-stranded pentanucleotide d(ACGCC): comparison with HIV-NCp7 complexes.
Related Articles NMR structure of the complex between the zinc finger protein NCp10 of Moloney murine leukemia virus and the single-stranded pentanucleotide d(ACGCC): comparison with HIV-NCp7 complexes.
Biochemistry. 1999 Oct 5;38(40):12984-94
Authors: Schüler W, Dong C, Wecker K, Roques BP
The structure of the 56 amino acid nucleocapsid protein NCp10 of...
nmrlearner
Journal club
0
11-18-2010 08:31 PM
[NMR paper] Characterization of the binding interface between ubiquitin and class I human ubiquit
Characterization of the binding interface between ubiquitin and class I human ubiquitin-conjugating enzyme 2b by multidimensional heteronuclear NMR spectroscopy in solution.
Related Articles Characterization of the binding interface between ubiquitin and class I human ubiquitin-conjugating enzyme 2b by multidimensional heteronuclear NMR spectroscopy in solution.
J Mol Biol. 1999 Jul 2;290(1):213-28
Authors: Miura T, Klaus W, Gsell B, Miyamoto C, Senn H
Ubiquitin-conjugating enzymes (Ubc) are involved in ubiquitination of proteins in the...
nmrlearner
Journal club
0
11-18-2010 08:31 PM
[NMR paper] Zinc- and sequence-dependent binding to nucleic acids by the N-terminal zinc finger o
Zinc- and sequence-dependent binding to nucleic acids by the N-terminal zinc finger of the HIV-1 nucleocapsid protein: NMR structure of the complex with the Psi-site analog, dACGCC.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Zinc- and sequence-dependent binding to nucleic acids by the N-terminal zinc finger of the HIV-1 nucleocapsid protein: NMR...
nmrlearner
Journal club
0
08-21-2010 11:53 PM
NMR Metabolomic Profiling Reveals New Roles of SUMOylation in DNA Damage Response.
NMR Metabolomic Profiling Reveals New Roles of SUMOylation in DNA Damage Response.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles NMR Metabolomic Profiling Reveals New Roles of SUMOylation in DNA Damage Response.
J Proteome Res. 2010 Aug 9;
Authors: Cano KE, Li YJ, Chen Y
Post-translational modifications by the Small Ubiquitin-like Modifier (SUMO) family of proteins have been established as critical events in the cellular response to a wide range of DNA damaging reagents and radiation;...
NMR structure of the human Rad18 zinc finger in complex with ubiquitin defines a class of UBZ domains in proteins linked to the DNA damage response.
Linear Mode
