1dsr
From Proteopedia
(New page: 200px<br /><applet load="1dsr" size="450" color="white" frame="true" align="right" spinBox="true" caption="1dsr" /> '''PEPTIDE ANTIBIOTIC, NMR, 6 STRUCTURES'''<br ...) |
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| - | [[Image:1dsr.jpg|left|200px]]<br /><applet load="1dsr" size=" | + | [[Image:1dsr.jpg|left|200px]]<br /><applet load="1dsr" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1dsr" /> | caption="1dsr" /> | ||
'''PEPTIDE ANTIBIOTIC, NMR, 6 STRUCTURES'''<br /> | '''PEPTIDE ANTIBIOTIC, NMR, 6 STRUCTURES'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The 3D structure of ramoplanin was studied by NMR spectroscopy in aqueous | + | The 3D structure of ramoplanin was studied by NMR spectroscopy in aqueous solution. A total of 320 interproton distances were determined from a NOESY spectrum and were used as restraints in distance geometry calculations. A structural refinement was carried out by molecular dynamics calculations in a solvent box. The structure of ramoplanin is characterized by two antiparallel beta-strands which are formed by the residues 2-7 and 10-14, respectively. The beta-strands are connected by six intramolecular hydrogen bonds and a reverse beta-turn which is formed by Thr8 and Phe9 (in positions i+1 and i+2, respectively). Residues 2 and 14 are connected by a loop consisting of Leu15, Ala16, Chp17, and the side chain of Asn2. Although residues 14-17 show the formation of a beta-turn, only the N-terminal end of the turn is directly connected to one of the beta-strands (Gly14), whereas the C-terminal end (Chp17) is linked via the side chain of Asn2. The 3D conformation of ramoplanin is also stabilized by a hydrophobic cluster of the aromatic sidechains of the residues 3, 9, and 17. This hydrophobic collapse leads to a U-shaped topology of the beta-shee: with the beta-turn at one end and the loop at the other end. The structure found for ramoplanin differs corsiderably from the published structure of ramoplanose which might be due to a smaller number of NOE distance restraints used in the previous study. |
==About this Structure== | ==About this Structure== | ||
| - | 1DSR is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Actinoplanes_sp. Actinoplanes sp.]. Full crystallographic information is available from [http:// | + | 1DSR is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Actinoplanes_sp. Actinoplanes sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DSR OCA]. |
==Reference== | ==Reference== | ||
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[[Category: ramoplanin]] | [[Category: ramoplanin]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:20:02 2008'' |
Revision as of 10:20, 21 February 2008
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PEPTIDE ANTIBIOTIC, NMR, 6 STRUCTURES
Overview
The 3D structure of ramoplanin was studied by NMR spectroscopy in aqueous solution. A total of 320 interproton distances were determined from a NOESY spectrum and were used as restraints in distance geometry calculations. A structural refinement was carried out by molecular dynamics calculations in a solvent box. The structure of ramoplanin is characterized by two antiparallel beta-strands which are formed by the residues 2-7 and 10-14, respectively. The beta-strands are connected by six intramolecular hydrogen bonds and a reverse beta-turn which is formed by Thr8 and Phe9 (in positions i+1 and i+2, respectively). Residues 2 and 14 are connected by a loop consisting of Leu15, Ala16, Chp17, and the side chain of Asn2. Although residues 14-17 show the formation of a beta-turn, only the N-terminal end of the turn is directly connected to one of the beta-strands (Gly14), whereas the C-terminal end (Chp17) is linked via the side chain of Asn2. The 3D conformation of ramoplanin is also stabilized by a hydrophobic cluster of the aromatic sidechains of the residues 3, 9, and 17. This hydrophobic collapse leads to a U-shaped topology of the beta-shee: with the beta-turn at one end and the loop at the other end. The structure found for ramoplanin differs corsiderably from the published structure of ramoplanose which might be due to a smaller number of NOE distance restraints used in the previous study.
About this Structure
1DSR is a Protein complex structure of sequences from Actinoplanes sp.. Full crystallographic information is available from OCA.
Reference
3D structure of ramoplanin: a potent inhibitor of bacterial cell wall synthesis., Kurz M, Guba W, Biochemistry. 1996 Sep 24;35(38):12570-5. PMID:8823194
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