BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > Educational resources > Journal club
Advanced Search



Jobs Groups Conferences Literature Pulse sequences Software forums Programs Sample preps Web resources BioNMR issues


Webservers
NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
Torsion angles from chemical shifts:
Preditor
TALOS
Promega- Proline
Secondary structure from chemical shifts:
CSI (via RCI server)
TALOS
MICS caps, β-turns
d2D
PECAN
Flexibility from chemical shifts:
RCI
Interactions from chemical shifts:
HADDOCK
Chemical shifts re-referencing:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
Quality Control Check
NMR spectrum prediction:
FANDAS
MestReS
V-NMR
Flexibility from structure:
Backbone S2
Methyl S2
B-factor
Molecular dynamics:
Gromacs
Amber
Antechamber
Chemical shifts prediction:
From structure:
Shiftx2
Sparta+
Camshift
CH3shift- Methyl
ArShift- Aromatic
ShiftS
Proshift
PPM
CheShift-2- Cα
From sequence:
Shifty
Camcoil
Poulsen_rc_CS
Disordered proteins:
MAXOCC
Format conversion & validation:
CCPN
From NMR-STAR 3.1
Validate NMR-STAR 3.1
NMR sample preparation:
Protein disorder:
DisMeta
Protein solubility:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


Reply
Thread Tools Search this Thread Rate Thread Display Modes
  #1  
Unread 08-28-2014, 10:09 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 19,995
Points: 193,617, Level: 100
Points: 193,617, Level: 100 Points: 193,617, Level: 100 Points: 193,617, Level: 100
Level up: 0%, 0 Points needed
Level up: 0% Level up: 0% Level up: 0%
Activity: 50.7%
Activity: 50.7% Activity: 50.7% Activity: 50.7%
Last Achievements
Award-Showcase
NMR Credits: 0
NMR Points: 193,617
Downloads: 0
Uploads: 0
Default 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.

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]



More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[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;...
nmrlearner Journal club 0 08-17-2010 03:36 AM


Thread Tools Search this Thread
Search this Thread:

Advanced Search
Display Modes Rate This Thread
Rate This Thread:

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is On
Trackbacks are Off
Pingbacks are Off
Refbacks are Off



BioNMR advertisements to pay for website hosting and domain registration. Nobody does it for us.



Powered by vBulletin® Version 3.7.3
Copyright ©2000 - 2020, Jelsoft Enterprises Ltd.
Copyright, BioNMR.com, 2003-2013
Search Engine Friendly URLs by vBSEO 3.6.0

All times are GMT. The time now is 03:57 AM.


Map