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
Home Forums Wiki NMR feeds Downloads Register Today's Posts



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  
Old 11-18-2010, 08:31 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,697
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 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 protein degradation pathway of eukaryotic cells. Ubc transfers the ubiquitin (Ub) molecules to target proteins by forming a thioester bond between their active site cysteine residue and the C-terminal glycine residue of ubiquitin. Here, we report on the NMR assignment and secondary structure of class I human ubiquitin-conjugating enzyme 2b (HsUbc2b). Chemical shift perturbation studies allowed us to map the contact area and binding interface between ubiquitin and HsUbc2b by1H-15N HSQC NMR spectroscopy. The serine mutant of the active site Cys88 of HsUbc2b was employed to obtain a relatively stable covalent ubiquitin complex of HsUbc2b(C88S). Changes in chemical shifts of amide protons and nitrogen atoms induced by the formation of the covalent complex were measured by preparing two segmentally labeled complexes with either ubiquitin or HsUbc2b(C88S)15N-labeled. In ubiquitin, the interaction is primarily sensed by the C-terminal segment Val70 - Gly76, and residues Lys48 and Gln49. The surface area on ubiquitin, as defined by these residues, overlaps partially with the presumed binding site with ubiquitin-activating enzyme (E1). In HsUbc2b, most of the affected residues cluster in the vicinity of the active site, namely, around the active site Cys88 itself, the second alpha-helix, and the flexible loop which connects helices alpha2 and alpha3 and which is adjacent to the active site. An additional site on HsUbc2b for a weak interaction with ubiquitin could be detected in a titration study where the two proteins were not covalently linked. This site is located on the backside of HsUbc2b opposite to the active site and is part of the beta-sheet. The covalent and non-covalent interaction sites are clearly separated on the HsUbc2b surface, while no such clear-cut segregation of the interaction area was observed on ubiquitin.

PMID: 10388568 [PubMed - indexed for MEDLINE]



Source: PubMed
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Zn-binding AZUL domain of human ubiquitin protein ligase Ube3A
Zn-binding AZUL domain of human ubiquitin protein ligase Ube3A Abstract Ube3A (also referred to as E6AP for E6 Associated Protein) is a E3 ubiquitin-protein ligase implicated in the development of Angelman syndrome by controlling degradation of synaptic protein Arc and oncogenic papilloma virus infection by controlling degradation of p53. This article describe the solution NMR structure of the conserved N-terminal domain of human Ube3A (residues 24-87) that contains two residues (Cys44 and Arg62) found to be mutated in patients with Angelman syndrome. The structure of this domain...
nmrlearner Journal club 0 09-30-2011 08:01 PM
[NMR paper] Over-expression and purification of isotopically labeled recombinant ligand-binding domain of orphan nuclear receptor human B1-binding factor/human liver receptor homologue 1 for NMR studies.
Over-expression and purification of isotopically labeled recombinant ligand-binding domain of orphan nuclear receptor human B1-binding factor/human liver receptor homologue 1 for NMR studies. Related Articles Over-expression and purification of isotopically labeled recombinant ligand-binding domain of orphan nuclear receptor human B1-binding factor/human liver receptor homologue 1 for NMR studies. Protein Expr Purif. 2006 Jan;45(1):99-106 Authors: Chen X, Tong X, Xie Y, Wang Y, Ma J, Gao D, Wu H, Chen H The human hepatitis B virus enhancer II...
nmrlearner Journal club 0 12-01-2010 06:56 PM
[NMR paper] Selective interface detection: mapping binding site contacts in membrane proteins by
Selective interface detection: mapping binding site contacts in membrane proteins by NMR spectroscopy. Related Articles Selective interface detection: mapping binding site contacts in membrane proteins by NMR spectroscopy. J Am Chem Soc. 2005 Apr 27;127(16):5734-5 Authors: Kiihne SR, Creemers AF, de Grip WJ, Bovee-Geurts PH, Lugtenburg J, de Groot HJ Intermolecular contact surfaces are important regions where specific interactions mediate biological function. We introduce a new magic angle spinning solid state NMR technique, dubbed "selective...
nmrlearner Journal club 0 11-25-2010 08:21 PM
[NMR paper] Biochemical and NMR mapping of the interface between CREB-binding protein and ligand
Biochemical and NMR mapping of the interface between CREB-binding protein and ligand binding domains of nuclear receptor: beyond the LXXLL motif. Related Articles Biochemical and NMR mapping of the interface between CREB-binding protein and ligand binding domains of nuclear receptor: beyond the LXXLL motif. J Biol Chem. 2005 Feb 18;280(7):5682-92 Authors: Klein FA, Atkinson RA, Potier N, Moras D, Cavarelli J CBP, cAMP-response element-binding protein (CREB)-binding protein, plays an important role as a general cointegrator of various signaling...
nmrlearner Journal club 0 11-24-2010 10:03 PM
[NMR paper] Defining the p53 DNA-binding domain/Bcl-x(L)-binding interface using NMR.
Defining the p53 DNA-binding domain/Bcl-x(L)-binding interface using NMR. Related Articles Defining the p53 DNA-binding domain/Bcl-x(L)-binding interface using NMR. FEBS Lett. 2004 Feb 13;559(1-3):171-4 Authors: Petros AM, Gunasekera A, Xu N, Olejniczak ET, Fesik SW p53 exerts its tumor suppressor activity through both transcription-dependent and transcription-independent processes. Although the transcription-dependent activity of p53 has been extensively studied, the mechanism for transcription-independent p53-mediated tumor suppression is...
nmrlearner Journal club 0 11-24-2010 09:25 PM
[NMR paper] Ubiquitin binding interface mapping on yeast ubiquitin hydrolase by NMR chemical shif
Ubiquitin binding interface mapping on yeast ubiquitin hydrolase by NMR chemical shift perturbation. Related Articles Ubiquitin binding interface mapping on yeast ubiquitin hydrolase by NMR chemical shift perturbation. Biochemistry. 1999 Jul 20;38(29):9242-53 Authors: Rajesh S, Sakamoto T, Iwamoto-Sugai M, Shibata T, Kohno T, Ito Y The interaction between the 26 kDa yeast ubiquitin hydrolase (YUH1), involved in maintaining the monomeric ubiquitin pool in cells, and the 8.5 kDa yeast ubiquitin protein has been studied by heteronuclear...
nmrlearner Journal club 0 11-18-2010 08:31 PM
[NMR paper] High-resolution heteronuclear NMR of human ubiquitin in an aqueous liquid crystalline
High-resolution heteronuclear NMR of human ubiquitin in an aqueous liquid crystalline medium. Related Articles High-resolution heteronuclear NMR of human ubiquitin in an aqueous liquid crystalline medium. J Biomol NMR. 1997 Oct;10(3):289-92 Authors: Bax A, Tjandra N A mixture of dihexanoyl phosphatidylcholine and dimyristoyl phosphatidylcholine in water forms disc-shaped particles, often referred to as bicelles . These adopt an ordered, liquid crystalline phase, which can be maintained at very low concentrations of the bicelles (down to 3%...
nmrlearner Journal club 0 08-22-2010 05:08 PM
[NMR paper] Solution structure of the carboxyl terminus of a human class Mu glutathione S-transfe
Solution structure of the carboxyl terminus of a human class Mu glutathione S-transferase: NMR assignment strategies in large proteins. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Solution structure of the carboxyl terminus of a human class Mu glutathione S-transferase: NMR assignment strategies in large proteins. J Mol Biol. 1999 Feb 5;285(5):2119-32 Authors: McCallum SA, Hitchens TK, Rule GS Strategies to obtain the NMR assignments for the HN, N, CO, Calpha and...
nmrlearner Journal club 0 08-21-2010 04:03 PM



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 - 2024, 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 09:38 PM.


Map