Solution NMR structure of VF0530 from Vibrio fischeri reveals a nucleic acid-binding function.

		BioNMR > Educational resources > Journal club
Solution NMR structure of VF0530 from Vibrio fischeri reveals a nucleic acid-binding function.

Webservers

NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

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:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

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:

Isotope labeling:

Solid-state NMR:

Thread Tools

Search this Thread

Rate Thread

Display Modes

09-10-2011, 06:51 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,777

Points: 193,617, Level: 100

Level up: 0%, 0 Points needed

Activity: 50.7%

Last Achievements

Award-Showcase

NMR Credits: 0

NMR Points: 193,617

Downloads: 0

Uploads: 0

Solution NMR structure of VF0530 from Vibrio fischeri reveals a nucleic acid-binding function.

Solution NMR structure of VF0530 from Vibrio fischeri reveals a nucleic acid-binding function.

Solution NMR structure of VF0530 from Vibrio fischeri reveals a nucleic acid-binding function.

Proteins. 2011 Oct;79(10):2988-91

Authors: Aramini JM, Rossi P, Fischer M, Xiao R, Acton TB, Montelione GT

Abstract
Protein domain family PF09905 (DUF2132) is a family of small domains of unknown function that are conserved in a wide range of bacteria. Here we describe the solution NMR structure of the 80-residue VF0530 protein from Vibrio fischeri, the first structural representative from this protein domain family. We demonstrate that the structure of VF0530 adopts a unique four-helix motif that shows some similarity to the C-terminal double-stranded DNA (dsDNA) binding domain of RecA, as well as other nucleic acid binding domains. Moreover, gel shift binding data indicate a potential dsDNA binding role for VF0530. Proteins 2011; © 2011 Wiley-Liss, Inc.

PMID: 21905121 [PubMed - in process]

Source: PubMed

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR images] Nucleic acid and protein NMR http://images.betterworldbooks.com/047/NMR-of-Proteins-and-Nucleic-Acids-9780471828938.jpg uoypuip.tumblr.com 11/11/2011 8:27:59 AM GMT Nucleic acid and protein NMR More...	nmrlearner	NMR pictures	0	11-12-2011 01:40 AM
A Solution NMR Study of the Interactions of Oligomannosides and the Anti-HIV-1 2G12 Antibody Reveals Distinct Binding Modes for Branched Ligands* A Solution NMR Study of the Interactions of Oligomannosides and the Anti-HIV-1 2G12 Antibody Reveals Distinct Binding Modes for Branched Ligands* A Solution NMR Study of the Interactions of Oligomannosides and the Anti-HIV-1 2G12 Antibody Reveals Distinct Binding Modes for Branched Ligands* Chemistry. 2011 Feb 1;17(5):1547-1560 Authors: Enríquez-Navas PM, Marradi M, Padro D, Angulo J, Penadés S The structural and affinity details of the interactions of synthetic oligomannosides, linear (di-, tri-, and tetra-) and branched (penta- and hepta-),...	nmrlearner	Journal club	0	01-27-2011 02:52 PM
A Solution NMR Study of the Interactions of Oligomannosides and the Anti-HIV-1 2G12 Antibody Reveals Distinct Binding Modes for Branched Ligands* A Solution NMR Study of the Interactions of Oligomannosides and the Anti-HIV-1 2G12 Antibody Reveals Distinct Binding Modes for Branched Ligands* A Solution NMR Study of the Interactions of Oligomannosides and the Anti-HIV-1 2G12 Antibody Reveals Distinct Binding Modes for Branched Ligands* Chemistry. 2011 Jan 5; Authors: Enríquez-Navas PM, Marradi M, Padro D, Angulo J, Penadés S The structural and affinity details of the interactions of synthetic oligomannosides, linear (di-, tri-, and tetra-) and branched (penta- and hepta-), with the broadly...	nmrlearner	Journal club	0	01-06-2011 11:21 AM
[NMR paper] NMR studies of protein-nucleic acid interactions. NMR studies of protein-nucleic acid interactions. Related Articles NMR studies of protein-nucleic acid interactions. Methods Mol Biol. 2004;278:289-312 Authors: Varani G, Chen Y, Leeper TC Protein-DNA and protein-RNA complexes play key functional roles in every living organism. Therefore, the elucidation of their structure and dynamics is an important goal of structural and molecular biology. Nuclear magnetic resonance (NMR) studies of protein and nucleic acid complexes have common features with studies of protein-protein complexes: the...	nmrlearner	Journal club	0	11-24-2010 09:25 PM
[NMR paper] NMR solution structure of type II human cellular retinoic acid binding protein: impli NMR solution structure of type II human cellular retinoic acid binding protein: implications for ligand binding. Related Articles NMR solution structure of type II human cellular retinoic acid binding protein: implications for ligand binding. Biochemistry. 1998 Sep 15;37(37):12727-36 Authors: Wang L, Li Y, Abildgaard F, Markley JL, Yan H The structure of human apo-cellular retinoic acid binding protein II (apo-CRABPII) in solution at pH 7.3 has been determined by NMR spectroscopy. The sequential assignments of the 1H, 13C, and 15N resonances...	nmrlearner	Journal club	0	11-17-2010 11:15 PM
[NMR paper] The NMR solution structure of intestinal fatty acid-binding protein complexed with pa The NMR solution structure of intestinal fatty acid-binding protein complexed with palmitate: application of a novel distance geometry algorithm. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles The NMR solution structure of intestinal fatty acid-binding protein complexed with palmitate: application of a novel distance geometry algorithm. J Mol Biol. 1996 Dec 6;264(3):585-602 Authors: Hodsdon ME, Ponder JW, Cistola DP The three-dimensional solution structure of rat...	nmrlearner	Journal club	0	08-22-2010 02:20 PM
[NMR paper] Multidimensional NMR spectroscopy of DNA-binding proteins: structure and function of Multidimensional NMR spectroscopy of DNA-binding proteins: structure and function of a transcription factor. Related Articles Multidimensional NMR spectroscopy of DNA-binding proteins: structure and function of a transcription factor. Toxicol Lett. 1995 Dec;82-83:577-89 Authors: Hsu VL, Jia X, Kearns DR The solution structure of a type II DNA-binding protein (DBPII), transcription factor 1 (TF1), has been determined using NMR spectroscopy. A multidimensional, heteronuclear strategy was employed to overcome assignment ambiguities due to...	nmrlearner	Journal club	0	08-22-2010 03:50 AM
[NMR paper] NMR - this other method for protein and nucleic acid structure determination. NMR - this other method for protein and nucleic acid structure determination. Related Articles NMR - this other method for protein and nucleic acid structure determination. Acta Crystallogr D Biol Crystallogr. 1995 May 1;51(Pt 3):249-70 Authors: WÃ¼thrich K For a quarter of a century X-ray diffraction in single crystals was unique in its ability to solve three-dimensional structures of proteins and nucleic acids at atomic resolution. The situation changed in 1984 with the completion of a protein structure determination by nuclear magnetic...	nmrlearner	Journal club	0	08-22-2010 03:41 AM

« Previous Thread | Next 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