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 08-21-2010, 04:03 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 17,589
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 and functional studies of the Mu repressor DNA-binding domain.

NMR structure and functional studies of the Mu repressor DNA-binding domain.

Related Articles NMR structure and functional studies of the Mu repressor DNA-binding domain.

Biochemistry. 1999 Jun 29;38(26):8367-76

Authors: Ilangovan U, Wojciak JM, Connolly KM, Clubb RT

The repressor protein of bacteriophage Mu establishes and maintains lysogeny by shutting down transposition functions needed for phage DNA replication. It interacts with several repeated DNA sequences within the early operator, preventing transcription from two divergent promoters. It also directly represses transposition by competing with the MuA transposase for an internal activation sequence (IAS) that is coincident with the operator and required for efficient transposition. The transposase and repressor proteins compete for the operator/IAS region using homologous DNA-binding domains located at their amino termini. Here we present the solution structure of the amino-terminal DNA-binding domain from the repressor protein determined by heteronuclear multidimensional nuclear magnetic resonance spectroscopy. The structure of the repressor DNA-binding domain provides insights into the molecular basis of several temperature sensitive mutations and, in combination with complementary experiments using flourescence anisotropy, surface plasmon resonance, and circular dichroism, defines the structural and biochemical differences between the transposase and repressor DNA-binding modules. We find that the repressor and enhancer domains possess similar three-dimensional structures, thermostabilities, and intrinsic affinities for DNA. This latter result suggests that the higher affinity of the full-length repressor relative to that of the MuA transposase protein originates from cooperative interactions between repressor protomers and not from intrinsic differences in their DNA-binding domains. In addition, we present the results of nucleotide and amino acid mutagenesis which delimits the minimal repressor DNA-binding module and coarsely defines the nucleotide dependence of repressor binding.

PMID: 10387082 [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
[NMR paper] NMR structures of salt-refolded forms of the 434-repressor DNA-binding domain in 6 M
NMR structures of salt-refolded forms of the 434-repressor DNA-binding domain in 6 M urea. Related Articles NMR structures of salt-refolded forms of the 434-repressor DNA-binding domain in 6 M urea. Biochemistry. 2004 Nov 9;43(44):13937-43 Authors: Pervushin K, Wider G, Iwai H, WŁthrich K The N-terminal 63-residue fragment of the phage 434-repressor, 434(1-63), has a well-defined globular fold in H(2)O solution, and is unfolded in 6 M urea at pH 7.5. In this study, 434(1-63) has been refolded by adding either 1.7 M NaCl or 0.47 M NaTFA to the...
nmrlearner Journal club 0 11-24-2010 10:03 PM
[NMR paper] Trp repressor-operator binding: NMR and electrophoretic mobility shift studies of the
Trp repressor-operator binding: NMR and electrophoretic mobility shift studies of the effect of DNA sequence and corepressor binding on two Trp repressor-operator complexes. Related Articles Trp repressor-operator binding: NMR and electrophoretic mobility shift studies of the effect of DNA sequence and corepressor binding on two Trp repressor-operator complexes. Biochemistry. 2002 Dec 17;41(50):14866-78 Authors: Jaseja M, Jeeves M, Hyde EI In Trp repressor-DNA complexes, most interactions either occur with phosphate groups or are...
nmrlearner Journal club 0 11-24-2010 08:58 PM
[NMR paper] Three-dimensional structure of the DNA-binding domain of the fructose repressor from
Three-dimensional structure of the DNA-binding domain of the fructose repressor from Escherichia coli by 1H and 15N NMR. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Three-dimensional structure of the DNA-binding domain of the fructose repressor from Escherichia coli by 1H and 15N NMR. J Mol Biol. 1997 Jul 18;270(3):496-510 Authors: Penin F, Geourjon C, Montserret R, Böckmann A, Lesage A, Yang YS, Bonod-Bidaud C, Cortay JC, Nègre D, Cozzone AJ, Deléage G FruR is...
nmrlearner Journal club 0 08-22-2010 05:08 PM
[NMR paper] NMR spectroscopic studies of the DNA-binding domain of the monomer-binding nuclear or
NMR spectroscopic studies of the DNA-binding domain of the monomer-binding nuclear orphan receptor, human estrogen related receptor-2. The carboxyl-terminal extension to the zinc-finger region is unstructured in the free form of the protein. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--highwire.stanford.edu-icons-externalservices-pubmed-standard-jbc_full_free.gif Related Articles NMR spectroscopic studies of the DNA-binding domain of the monomer-binding nuclear orphan receptor, human estrogen related receptor-2. The carboxyl-terminal extension to the zinc-finger region...
nmrlearner Journal club 0 08-22-2010 05:08 PM
[NMR paper] Solution structure of the LexA repressor DNA binding domain determined by 1H NMR spec
Solution structure of the LexA repressor DNA binding domain determined by 1H NMR spectroscopy. 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 the LexA repressor DNA binding domain determined by 1H NMR spectroscopy. EMBO J. 1994 Sep 1;13(17):3936-44 Authors: Fogh RH, Ottleben G, R√ľterjans H, Schnarr M, Boelens R, Kaptein R The structure of the 84 residue DNA binding domain of the Escherichia coli LexA repressor has been determined from...
nmrlearner Journal club 0 08-22-2010 03:29 AM
[NMR paper] NMR studies of the POU-specific DNA-binding domain of Oct-1: sequential 1H and 15N as
NMR studies of the POU-specific DNA-binding domain of Oct-1: sequential 1H and 15N assignments and secondary structure. Related Articles NMR studies of the POU-specific DNA-binding domain of Oct-1: sequential 1H and 15N assignments and secondary structure. Biochemistry. 1993 Jun 15;32(23):6032-40 Authors: Cox M, Dekker N, Boelens R, Verrijzer CP, van der Vliet PC, Kaptein R The 1H and 15N resonances of the POU-specific DNA-binding domain of transcription factor Oct-1 have been assigned sequentially using two-dimensional homo- and heteronuclear...
nmrlearner Journal club 0 08-21-2010 11:53 PM
[NMR paper] Secondary structure of the homeo domain of yeast alpha 2 repressor determined by NMR
Secondary structure of the homeo domain of yeast alpha 2 repressor determined by NMR spectroscopy. Related Articles Secondary structure of the homeo domain of yeast alpha 2 repressor determined by NMR spectroscopy. Genes Dev. 1991 May;5(5):764-72 Authors: Phillips CL, Vershon AK, Johnson AD, Dahlquist FW The yeast alpha 2 protein is a regulator of cell type in Saccharomyces cerevisiae. It represses transcription of a set of target genes by binding to an operator located upstream of each of these genes. The alpha 2 protein shares weak sequence...
nmrlearner Journal club 0 08-21-2010 11:16 PM
Robust structure-based resonance assignment for functional protein studies by NMR
Abstract High-throughput functional protein NMR studies, like protein interactions or dynamics, require an automated approach for the assignment of the protein backbone. With the availability of a growing number of protein 3D structures, a new class of automated approaches, called structure-based assignment, has been developed quite recently. Structure-based approaches use primarily NMR input data that are not based on J-coupling and for which connections between residues are not limited by through bonds magnetization transfer efficiency. We present here a robust structure-based assignment...
nmrlearner Journal club 0 08-14-2010 04:19 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 - 2017, 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 08:02 AM.


Map