NMR paper NMR structure of the Tn916 integrase-DNA complex.

		BioNMR > Educational resources > Journal club
[NMR paper] NMR structure of the Tn916 integrase-DNA complex.

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:

View First Unread

Thread Tools

Search this Thread

Rate Thread

Display Modes

08-21-2010, 04:03 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,174

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

NMR structure of the Tn916 integrase-DNA complex.

NMR structure of the Tn916 integrase-DNA complex.

Related Articles NMR structure of the Tn916 integrase-DNA complex.

Nat Struct Biol. 1999 Apr;6(4):366-73

Authors: Wojciak JM, Connolly KM, Clubb RT

The integrase protein catalyzes the excision and integration of the Tn916 conjugative transposon, a promiscuous genetic element that spreads antibiotic resistance in pathogenic bacteria. The solution structure of the N-terminal domain of the Tn916 integrase protein bound to its DNA-binding site within the transposon arm has been determined. The structure reveals an interesting mode of DNA recognition, in which the face of a three-stranded antiparallel beta-sheet is positioned within the major groove. A comparison to the structure of the homing endonuclease I-Ppol-DNA complex suggests that the three-stranded sheet may represent a new DNA-binding motif whose residue composition and position within the major groove are varied to alter specificity. The structure also provides insights into the mechanism of conjugative transposition. The DNA in the complex is bent approximately 35 degrees and may, together with potential interactions between bound integrase proteins at directly repeated sites, significantly bend the arms of the transposon.

PMID: 10201406 [PubMed - indexed for MEDLINE]

Source: PubMed

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] Towards a structure for a TSG-6.hyaluronan complex by modeling and NMR spectroscopy: Towards a structure for a TSG-6.hyaluronan complex by modeling and NMR spectroscopy: insights into other members of the link module superfamily. Related Articles Towards a structure for a TSG-6.hyaluronan complex by modeling and NMR spectroscopy: insights into other members of the link module superfamily. J Biol Chem. 2005 May 6;280(18):18189-201 Authors: Blundell CD, Almond A, Mahoney DJ, DeAngelis PL, Campbell ID, Day AJ The Link module from human TSG-6, a hyaladherin with roles in ovulation and inflammation, has a hyaluronan (HA)-binding...	nmrlearner	Journal club	0	11-24-2010 11:14 PM
NMR Solution Structure of a DNA-Actinomycin D Complex Containing a Non-Hydrogen-Bondi NMR Solution Structure of a DNA-Actinomycin D Complex Containing a Non-Hydrogen-Bonding Pair in the Binding Site Shannen L. Cravens, Alyssa C. Navapanich, Bernhard H. Geierstanger, Deborah C. Tahmassebi and Tammy J. Dwyer http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja107575f/aop/images/medium/ja-2010-07575f_0011.gif Journal of the American Chemical Society DOI: 10.1021/ja107575f http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/tQROiStkm5c	nmrlearner	Journal club	0	11-23-2010 07:10 AM
[NMR paper] The NMR structure of the 38 kDa U1A protein - PIE RNA complex reveals the basis of co The NMR structure of the 38 kDa U1A protein - PIE RNA complex reveals the basis of cooperativity in regulation of polyadenylation by human U1A protein. Related Articles The NMR structure of the 38 kDa U1A protein - PIE RNA complex reveals the basis of cooperativity in regulation of polyadenylation by human U1A protein. Nat Struct Biol. 2000 Apr;7(4):329-35 Authors: Varani L, Gunderson SI, Mattaj IW, Kay LE, Neuhaus D, Varani G The status of the poly(A) tail at the 3'-end of mRNAs controls the expression of numerous genes in response to...	nmrlearner	Journal club	0	11-18-2010 09:15 PM
[NMR paper] Determination of the NMR structure of the complex between U1A protein and its RNA pol Determination of the NMR structure of the complex between U1A protein and its RNA polyadenylation inhibition element. Related Articles Determination of the NMR structure of the complex between U1A protein and its RNA polyadenylation inhibition element. J Biomol NMR. 1998 Jan;11(1):59-84 Authors: Howe PW, Allain FH, Varani G, Neuhaus D RNA-protein recognition is critical to post-transcriptional regulation of gene expression, yet poorly understood at the molecular level. The relatively slow progress in understanding this important area of...	nmrlearner	Journal club	0	11-17-2010 11:06 PM
[NMR paper] Correction of the NMR structure of the ETS1/DNA complex. Correction of the NMR structure of the ETS1/DNA complex. Related Articles Correction of the NMR structure of the ETS1/DNA complex. J Biomol NMR. 1997 Dec;10(4):317-28 Authors: Werner MH, Clore GM, Fisher CL, Fisher RJ, Trinh L, Shiloach J, Gronenborn AM The ETS family of transcription factors consists of a group of proteins that share a highly conserved 85 amino acid DNA-binding domain (DBD). This family recognizes a consensus sequence rich in purine bases with a central GGAA motif. A comparison of the published three-dimensional structures of...	nmrlearner	Journal club	0	08-22-2010 05:08 PM
[NMR paper] Determination of the NMR solution structure of a specific DNA complex of the Myb DNA- Determination of the NMR solution structure of a specific DNA complex of the Myb DNA-binding domain. Related Articles Determination of the NMR solution structure of a specific DNA complex of the Myb DNA-binding domain. J Biomol NMR. 1995 Nov;6(3):294-305 Authors: Morikawa S, Ogata K, Sekikawa A, Sarai A, Ishii S, Nishimura Y, Nakamura H The solution structure of a specific DNA complex of the minimum DNA-binding domain of the mouse c-Myb protein was determined by distance geometry calculations using a set of 1732 nuclear Overhauser enhancement...	nmrlearner	Journal club	0	08-22-2010 03:50 AM
[NMR paper] NMR structure of a specific DNA complex of Zn-containing DNA binding domain of GATA-1 NMR structure of a specific DNA complex of Zn-containing DNA binding domain of GATA-1. Related Articles NMR structure of a specific DNA complex of Zn-containing DNA binding domain of GATA-1. Science. 1993 Jul 23;261(5120):438-46 Authors: Omichinski JG, Clore GM, Schaad O, Felsenfeld G, Trainor C, Appella E, Stahl SJ, Gronenborn AM The three-dimensional solution structure of a complex between the DNA binding domain of the chicken erythroid transcription factor GATA-1 and its cognate DNA site has been determined with multidimensional...	nmrlearner	Journal club	0	08-22-2010 03:01 AM
[NMR paper] The three-dimensional structure of the vnd/NK-2 homeodomain-DNA complex by NMR spectr The three-dimensional structure of the vnd/NK-2 homeodomain-DNA complex by NMR spectroscopy. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles The three-dimensional structure of the vnd/NK-2 homeodomain-DNA complex by NMR spectroscopy. J Mol Biol. 1999 Jun 11;289(3):529-45 Authors: Gruschus JM, Tsao DH, Wang LH, Nirenberg M, Ferretti JA The three-dimensional solution structure obtained by NMR of the complex formed between the uniformly singly15N and doubly13C/15N-labeled...	nmrlearner	Journal club	0	08-21-2010 04:03 PM

« 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