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 08-21-2010, 11:45 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,700
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 Solution structure of the phosphocarrier protein HPr from Bacillus subtilis by two-di

Solution structure of the phosphocarrier protein HPr from Bacillus subtilis by two-dimensional NMR spectroscopy.

Related Articles Solution structure of the phosphocarrier protein HPr from Bacillus subtilis by two-dimensional NMR spectroscopy.

Protein Sci. 1992 Oct;1(10):1363-76

Authors: Wittekind M, Rajagopal P, Branchini BR, Reizer J, Saier MH, Klevit RE

The solution structure of the phosphocarrier protein, HPr, from Bacillus subtilis has been determined by analysis of two-dimensional (2D) NMR spectra acquired for the unphosphorylated form of the protein. Inverse-detected 2D (1H-15N) heteronuclear multiple quantum correlation nuclear Overhauser effect (HMQC NOESY) and homonuclear Hartmann-Hahn (HOHAHA) spectra utilizing 15N assignments (reported here) as well as previously published 1H assignments were used to identify cross-peaks that are not resolved in 2D homonuclear 1H spectra. Distance constraints derived from NOESY cross-peaks, hydrogen-bonding patterns derived from 1H-2H exchange experiments, and dihedral angle constraints derived from analysis of coupling constants were used for structure calculations using the variable target function algorithm, DIANA. The calculated models were refined by dynamical simulated annealing using the program X-PLOR. The resulting family of structures has a mean backbone rmsd of 0.63 A (N, C alpha, C', O atoms), excluding the segments containing residues 45-59 and 84-88. The structure is comprised of a four-stranded antiparallel beta-sheet with two antiparallel alpha-helices on one side of the sheet. The active-site His 15 residue serves as the N-cap of alpha-helix A, with its N delta 1 atom pointed toward the solvent to accept the phosphoryl group during the phosphotransfer reaction with enzyme I. The existence of a hydrogen bond between the side-chain oxygen atom of Tyr 37 and the amide proton of Ala 56 is suggested, which may account for the observed stabilization of the region that includes the beta-turn comprised of residues 37-40. If the beta alpha beta beta alpha beta (alpha) folding topology of HPr is considered with the peptide chain polarity reversed, the protein fold is identical to that described for another group of beta alpha beta beta alpha beta proteins that include acylphosphatase and the RNA-binding domains of the U1 snRNP A and hnRNP C proteins.

PMID: 1303754 [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 resonance assignment of the autoimmunity protein SpaI from Bacillus subtilis ATCC 6633.
NMR resonance assignment of the autoimmunity protein SpaI from Bacillus subtilis ATCC 6633. NMR resonance assignment of the autoimmunity protein SpaI from Bacillus subtilis ATCC 6633. Biomol NMR Assign. 2011 Jun 5; Authors: Christ NA, Duchardt-Ferner E, Düsterhus S, Kötter P, Entian KD, Wöhnert J Bacillus subtilis ATCC 6633 produces the lipid II targeting lantibiotic subtilin. For self-protection these gram-positive bacteria express a cluster of four self-immunity proteins named SpaIFEG. SpaI is a 16.8*kDa lipoprotein which is attached to the...
nmrlearner Journal club 0 06-07-2011 11:05 AM
[NMR paper] NMR assignment of new thioredoxin-like protein YkuV from Bacillus subtilis.
NMR assignment of new thioredoxin-like protein YkuV from Bacillus subtilis. Related Articles NMR assignment of new thioredoxin-like protein YkuV from Bacillus subtilis. J Biomol NMR. 2005 Jul;32(3):258 Authors: Zhang X, Yu C, Xia B, Jin C
nmrlearner Journal club 0 12-01-2010 06:56 PM
[NMR paper] Interaction of the replication terminator protein of Bacillus subtilis with DNA probed by NMR spectroscopy.
Interaction of the replication terminator protein of Bacillus subtilis with DNA probed by NMR spectroscopy. Related Articles Interaction of the replication terminator protein of Bacillus subtilis with DNA probed by NMR spectroscopy. Biochem Biophys Res Commun. 2005 Sep 23;335(2):361-6 Authors: Hastings AF, Otting G, Folmer RH, Duggin IG, Wake RG, Wilce MC, Wilce JA Termination of DNA replication in Bacillus subtilis involves the polar arrest of replication forks by a specific complex formed between the dimeric 29 kDa replication terminator...
nmrlearner Journal club 0 12-01-2010 06:56 PM
[NMR paper] Solution structure of the peptidoglycan binding domain of Bacillus subtilis cell wall lytic enzyme CwlC: characterization of the sporulation-related repeats by NMR.
Solution structure of the peptidoglycan binding domain of Bacillus subtilis cell wall lytic enzyme CwlC: characterization of the sporulation-related repeats by NMR. Related Articles Solution structure of the peptidoglycan binding domain of Bacillus subtilis cell wall lytic enzyme CwlC: characterization of the sporulation-related repeats by NMR. Biochemistry. 2005 Aug 2;44(30):10153-63 Authors: Mishima M, Shida T, Yabuki K, Kato K, Sekiguchi J, Kojima C Bacillus subtilis CwlC is a cell wall lytic N-acetylmuramoyl-l-alanine amidase that plays an...
nmrlearner Journal club 0 12-01-2010 06:56 PM
[NMR paper] Crystallization of the Bacillus subtilis RTP-DNA complex prepared using NMR spectrosc
Crystallization of the Bacillus subtilis RTP-DNA complex prepared using NMR spectroscopy. Related Articles Crystallization of the Bacillus subtilis RTP-DNA complex prepared using NMR spectroscopy. Acta Crystallogr D Biol Crystallogr. 2001 Mar;57(Pt 3):421-4 Authors: Vivian JP, Wilce JA, Hastings AF, Wilce MC The replication terminator protein (RTP)-DNA complex of Bacillus subtilis is responsible for the arrest of DNA replication at terminator sites in the B. subtilis chromosome. The crystallization and preliminary diffraction data analysis...
nmrlearner Journal club 0 11-19-2010 08:32 PM
Probing the Folding Intermediate of Bacillus subtilis RNase P protein by NMR.
Probing the Folding Intermediate of Bacillus subtilis RNase P protein by NMR. Related Articles Probing the Folding Intermediate of Bacillus subtilis RNase P protein by NMR. Biochemistry. 2010 Sep 15; Authors: Chang YC, Franch WR, Oas TG Protein folding intermediates are often imperative to overall folding processes and consequent biological functions. However, the low population and transient nature of the intermediate states often hinder the biochemical and biophysical characterization. Previous studies have demonstrated that Bacillus...
nmrlearner Journal club 0 09-17-2010 04:14 PM
[NMR paper] High-resolution NMR structure and backbone dynamics of the Bacillus subtilis response
High-resolution NMR structure and backbone dynamics of the Bacillus subtilis response regulator, Spo0F: implications for phosphorylation and molecular recognition. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles High-resolution NMR structure and backbone dynamics of the Bacillus subtilis response regulator, Spo0F: implications for phosphorylation and molecular recognition. Biochemistry. 1997 Aug 19;36(33):10015-25 Authors: Feher VA, Zapf JW, Hoch JA, Whiteley JM, McIntosh LP, Rance M, Skelton NJ,...
nmrlearner Journal club 0 08-22-2010 05:08 PM
[NMR paper] Low resolution solution structure of the Bacillus subtilis glucose permease IIA domai
Low resolution solution structure of the Bacillus subtilis glucose permease IIA domain derived from heteronuclear three-dimensional NMR spectroscopy. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Low resolution solution structure of the Bacillus subtilis glucose permease IIA domain derived from heteronuclear three-dimensional NMR spectroscopy. FEBS Lett. 1992 Jan 20;296(2):148-52 Authors: Fairbrother WJ, Gippert GP, Reizer J, Saier MH, Wright PE A low resolution...
nmrlearner Journal club 0 08-21-2010 11:41 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 09:23 AM.


Map