1r9u: Difference between revisions

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New page: left|200px<br /><applet load="1r9u" size="450" color="white" frame="true" align="right" spinBox="true" caption="1r9u" /> '''Refined structure of peptaibol zervamicin II...
 
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[[Image:1r9u.gif|left|200px]]<br /><applet load="1r9u" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1r9u" />
'''Refined structure of peptaibol zervamicin IIB in methanol solution from trans-hydrogen bond J couplings'''<br />


==Overview==
==Refined structure of peptaibol zervamicin IIB in methanol solution from trans-hydrogen bond J couplings==
Zervamicin IIB (Zrv-IIB) is a channel-forming peptaibol antibiotic of, fungal origin. The measured transhydrogen bond (3h)J(NC') couplings in, methanol solution heaving average value of -0.41 Hz indicate that the, stability of the Zrv-IIB helix in this milieu is comparable to the, stability of helices in globular proteins. The N-terminus of the peptide, forms an alpha-helix, whereas 3(10)-helical hydrogen bonds stabilize the, C-terminus. However, two weak transhydrogen bond peaks are observed in a, long-range HNCO spectrum for HN Aib(12). Energy calculations using the, Empirical Conformation Energy Program for Peptides (ECEPP)/2 force field, and the implicit solvent model show that the middle of the peptide helix, accommodates a bifurcated hydrogen bond that is simultaneously formed, between HN Aib(12) and CO Leu(8) and CO Aib(9). Several lowered (3h)J(NC'), on a polar face of the helix correlate with the conformational exchange, process observed earlier and imply dynamic distortions of a hydrogen bond, pattern with the predominant population of a properly folded helical, structure. The refined structure of Zrv-IIB on the basis of the observed, hydrogen bond pattern has a small ( approximately 20 degrees ) angle of, helix bending that is virtually identical to the angle of bending in, dodecylphosphocholine (DPC) micelles, indicating the stability of a hinge, region in different environments. NMR parameters ((1)HN chemical shifts, and transpeptide bond (1)J(NC') couplings) sensitive to hydrogen bonding, along with the solvent accessible surface area of carbonyl oxygens, indicate a large polar patch on the convex side of the helix formed by, three exposed backbone carbonyls of Aib(7), Aib(9), and Hyp(10) and polar, side chains of Hyp(10), Gln(11), and Hyp(13). The unique structural, features, high helix stability and the enhanced polar patch, set apart, Zrv-IIB from other peptaibols (for example, alamethicin) and possibly, underlie its biological and physiological properties.
<StructureSection load='1r9u' size='340' side='right'caption='[[1r9u]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1r9u]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Emericellopsis_salmosynnemata Emericellopsis salmosynnemata]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R9U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1R9U FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=AIB:ALPHA-AMINOISOBUTYRIC+ACID'>AIB</scene>, <scene name='pdbligand=DIV:D-ISOVALINE'>DIV</scene>, <scene name='pdbligand=HYP:4-HYDROXYPROLINE'>HYP</scene>, <scene name='pdbligand=PHL:L-PHENYLALANINOL'>PHL</scene>, <scene name='pdbligand=PRD_000159:Zervamicin+IIB'>PRD_000159</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1r9u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r9u OCA], [https://pdbe.org/1r9u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1r9u RCSB], [https://www.ebi.ac.uk/pdbsum/1r9u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1r9u ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Zervamicin IIB is a member of the alpha-aminoisobutyric acid containing peptaibol antibiotics. A new procedure for the biosynthetic preparation of the uniformly 13C- and 15N-enriched peptaibol is described This compound was isolated from the biomass of the fungus-producer Emericellopsis salmosynnemata strain 336 IMI 58330 obtained upon cultivation in the totally 13C, 15N-labelled complete medium. To prepare such a medium the autolysed biomass and the exopolysaccharides of the obligate methylotrophic bacterium Methylobacillus flagellatus KT were used. This microorganism was grown in totally 13C, 15N-labelled minimal medium containing 13C-methanol and 15N-ammonium chloride as the only carbon and nitrogen sources. Preliminary NMR spectroscopic analysis indicated a high extent of isotope incorporation (&gt; 90%) and led to the complete 13C- and 15N-NMR assignment including the stereospecific assignment of Aib residues methyl groups. The observed pattern of the structurally important secondary chemical shifts of 1H(alpha), 13C=O and 13C(alpha) agrees well with the previously determined structure of zervamicin IIB in methanol solution.


==About this Structure==
Biosynthetic uniform 13C,15N-labelling of zervamicin IIB. Complete 13C and 15N NMR assignment.,Ovchinnikova TV, Shenkarev ZO, Yakimenko ZA, Svishcheva NV, Tagaev AA, Skladnev DA, Arseniev AS J Pept Sci. 2003 Nov-Dec;9(11-12):817-26. PMID:14658801<ref>PMID:14658801</ref>
1R9U is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Emericellopsis_salmosynnemata Emericellopsis salmosynnemata] with ACE as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1R9U OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Peptaibol zervamicin IIb structure and dynamics refinement from transhydrogen bond J couplings., Shenkarev ZO, Balashova TA, Yakimenko ZA, Ovchinnikova TV, Arseniev AS, Biophys J. 2004 Jun;86(6):3687-99. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15189865 15189865]
</div>
<div class="pdbe-citations 1r9u" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Emericellopsis salmosynnemata]]
[[Category: Emericellopsis salmosynnemata]]
[[Category: Protein complex]]
[[Category: Large Structures]]
[[Category: Arseniev, A.S.]]
[[Category: Arseniev AS]]
[[Category: Balashova, T.A.]]
[[Category: Balashova TA]]
[[Category: Ovchinnikova, T.V.]]
[[Category: Ovchinnikova TV]]
[[Category: Shenkarev, Z.O.]]
[[Category: Shenkarev ZO]]
[[Category: Yakimenko, Z.A.]]
[[Category: Yakimenko ZA]]
[[Category: ACE]]
[[Category: bent helix]]
[[Category: bifurcated hydrogen bond]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 22:24:52 2007''

Latest revision as of 16:58, 1 February 2024

Refined structure of peptaibol zervamicin IIB in methanol solution from trans-hydrogen bond J couplingsRefined structure of peptaibol zervamicin IIB in methanol solution from trans-hydrogen bond J couplings

Structural highlights

1r9u is a 1 chain structure with sequence from Emericellopsis salmosynnemata. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Solution NMR
Ligands:, , , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

Zervamicin IIB is a member of the alpha-aminoisobutyric acid containing peptaibol antibiotics. A new procedure for the biosynthetic preparation of the uniformly 13C- and 15N-enriched peptaibol is described This compound was isolated from the biomass of the fungus-producer Emericellopsis salmosynnemata strain 336 IMI 58330 obtained upon cultivation in the totally 13C, 15N-labelled complete medium. To prepare such a medium the autolysed biomass and the exopolysaccharides of the obligate methylotrophic bacterium Methylobacillus flagellatus KT were used. This microorganism was grown in totally 13C, 15N-labelled minimal medium containing 13C-methanol and 15N-ammonium chloride as the only carbon and nitrogen sources. Preliminary NMR spectroscopic analysis indicated a high extent of isotope incorporation (> 90%) and led to the complete 13C- and 15N-NMR assignment including the stereospecific assignment of Aib residues methyl groups. The observed pattern of the structurally important secondary chemical shifts of 1H(alpha), 13C=O and 13C(alpha) agrees well with the previously determined structure of zervamicin IIB in methanol solution.

Biosynthetic uniform 13C,15N-labelling of zervamicin IIB. Complete 13C and 15N NMR assignment.,Ovchinnikova TV, Shenkarev ZO, Yakimenko ZA, Svishcheva NV, Tagaev AA, Skladnev DA, Arseniev AS J Pept Sci. 2003 Nov-Dec;9(11-12):817-26. PMID:14658801[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

  1. ↑ Ovchinnikova TV, Shenkarev ZO, Yakimenko ZA, Svishcheva NV, Tagaev AA, Skladnev DA, Arseniev AS. Biosynthetic uniform 13C,15N-labelling of zervamicin IIB. Complete 13C and 15N NMR assignment. J Pept Sci. 2003 Nov-Dec;9(11-12):817-26. PMID:14658801 doi:10.1002/psc.499
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