3e7r: Difference between revisions

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[[Image:3e7r.png|left|200px]]


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==X-ray Crystal Structure of Racemic Plectasin==
The line below this paragraph, containing "STRUCTURE_3e7r", creates the "Structure Box" on the page.
<StructureSection load='3e7r' size='340' side='right'caption='[[3e7r]], [[Resolution|resolution]] 1.00&Aring;' scene=''>
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== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[3e7r]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudoplectania_nigrella Pseudoplectania nigrella]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E7R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3E7R FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3e7r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e7r OCA], [https://pdbe.org/3e7r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3e7r RCSB], [https://www.ebi.ac.uk/pdbsum/3e7r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3e7r ProSAT]</span></td></tr>
{{STRUCTURE_3e7r|  PDB=3e7r  |  SCENE=  }}
</table>
== Function ==
[https://www.uniprot.org/uniprot/DEFPL_PSENR DEFPL_PSENR] Antimicrobial peptide that potently acts against several species of Gram-positive bacteria (PubMed:16222292, PubMed:19472324). It selectively inhibits peptidoglycan biosynthesis through complex formation with the cell wall precursor lipid II (1:1 molar ratio) thus inhibiting cell wall synthesis (PubMed:20508130). It does not disrupt cell membranes (PubMed:20508130). Is especially active against numerous clinical isolates of S.pneumoniae, including all 90 different serotypes and isolates resistant to clinically used antibiotics (PubMed:16222292). In vitro, shows considerable selectivity for bacteria over mammalian cells (PubMed:16222292). The peptide synthesized in D-amino acids does not show antibacterial activity (PubMed:19472324). In vitro, acts on voltage-gated potassium channels by moderately inhibiting mammalian Kv1.3/KCNA3 (IC(50)=2.8 uM), and moderately inhibiting others potassium channels (PubMed:25568977).<ref>PMID:16222292</ref> <ref>PMID:25568977</ref>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
We describe the use of racemic crystallography to determine the X-ray structure of the natural product plectasin, a potent antimicrobial protein recently isolated from fungus. The protein enantiomers L-plectasin and D-plectasin were prepared by total chemical synthesis; interestingly, L-plectasin showed the expected antimicrobial activity, while D-plectasin was devoid of such activity. The mirror image proteins were then used for racemic crystallization. Synchrotron X-ray diffraction data were collected to atomic resolution from a racemic plectasin crystal; the racemate crystallized in the achiral centrosymmetric space group P1 with one L-plectasin molecule and one D-plectasin molecule forming the unit cell. Dimer-like intermolecular interactions between the protein enantiomers were observed, which may account for the observed extremely low solvent content (13%-15%) and more highly ordered nature of the racemic crystals. The structure of the plectasin molecule was well defined for all 40 amino acids and was generally similar to the previously determined NMR structure, suggesting minimal impact of the crystal packing on the plectasin conformation.


===X-ray Crystal Structure of Racemic Plectasin===
Racemic crystallography of synthetic protein enantiomers used to determine the X-ray structure of plectasin by direct methods.,Mandal K, Pentelute BL, Tereshko V, Thammavongsa V, Schneewind O, Kossiakoff AA, Kent SB Protein Sci. 2009 Jun;18(6):1146-54. PMID:19472324<ref>PMID:19472324</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 3e7r" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 19472324 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_19472324}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
[[3e7r]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E7R OCA].
[[Category: Pseudoplectania nigrella]]
 
[[Category: Kent SBH]]
==Reference==
[[Category: Kossiakoff AA]]
<ref group="xtra">PMID:019472324</ref><references group="xtra"/>
[[Category: Mandal K]]
[[Category: Kent, S B.H.]]
[[Category: Pentelute BL]]
[[Category: Kossiakoff, A A.]]
[[Category: Tereshko V]]
[[Category: Mandal, K.]]
[[Category: Pentelute, B L.]]
[[Category: Tereshko, V.]]
[[Category: Antibiotic]]
[[Category: Antimicrobial]]
[[Category: Antimicrobial protein]]
[[Category: Cleavage on pair of basic residue]]
[[Category: Defensin]]
[[Category: Plectasin]]
[[Category: Racemic protein crystallography]]
[[Category: Secreted]]

Latest revision as of 08:46, 17 October 2024

X-ray Crystal Structure of Racemic PlectasinX-ray Crystal Structure of Racemic Plectasin

Structural highlights

3e7r is a 1 chain structure with sequence from Pseudoplectania nigrella. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DEFPL_PSENR Antimicrobial peptide that potently acts against several species of Gram-positive bacteria (PubMed:16222292, PubMed:19472324). It selectively inhibits peptidoglycan biosynthesis through complex formation with the cell wall precursor lipid II (1:1 molar ratio) thus inhibiting cell wall synthesis (PubMed:20508130). It does not disrupt cell membranes (PubMed:20508130). Is especially active against numerous clinical isolates of S.pneumoniae, including all 90 different serotypes and isolates resistant to clinically used antibiotics (PubMed:16222292). In vitro, shows considerable selectivity for bacteria over mammalian cells (PubMed:16222292). The peptide synthesized in D-amino acids does not show antibacterial activity (PubMed:19472324). In vitro, acts on voltage-gated potassium channels by moderately inhibiting mammalian Kv1.3/KCNA3 (IC(50)=2.8 uM), and moderately inhibiting others potassium channels (PubMed:25568977).[1] [2]

Publication Abstract from PubMed

We describe the use of racemic crystallography to determine the X-ray structure of the natural product plectasin, a potent antimicrobial protein recently isolated from fungus. The protein enantiomers L-plectasin and D-plectasin were prepared by total chemical synthesis; interestingly, L-plectasin showed the expected antimicrobial activity, while D-plectasin was devoid of such activity. The mirror image proteins were then used for racemic crystallization. Synchrotron X-ray diffraction data were collected to atomic resolution from a racemic plectasin crystal; the racemate crystallized in the achiral centrosymmetric space group P1 with one L-plectasin molecule and one D-plectasin molecule forming the unit cell. Dimer-like intermolecular interactions between the protein enantiomers were observed, which may account for the observed extremely low solvent content (13%-15%) and more highly ordered nature of the racemic crystals. The structure of the plectasin molecule was well defined for all 40 amino acids and was generally similar to the previously determined NMR structure, suggesting minimal impact of the crystal packing on the plectasin conformation.

Racemic crystallography of synthetic protein enantiomers used to determine the X-ray structure of plectasin by direct methods.,Mandal K, Pentelute BL, Tereshko V, Thammavongsa V, Schneewind O, Kossiakoff AA, Kent SB Protein Sci. 2009 Jun;18(6):1146-54. PMID:19472324[3]

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

References

  1. ↑ Mygind PH, Fischer RL, Schnorr KM, Hansen MT, Sonksen CP, Ludvigsen S, Raventos D, Buskov S, Christensen B, De Maria L, Taboureau O, Yaver D, Elvig-Jorgensen SG, Sorensen MV, Christensen BE, Kjaerulff S, Frimodt-Moller N, Lehrer RI, Zasloff M, Kristensen HH. Plectasin is a peptide antibiotic with therapeutic potential from a saprophytic fungus. Nature. 2005 Oct 13;437(7061):975-80. PMID:16222292 doi:nature04051
  2. ↑ Xiang F, Xie Z, Feng J, Yang W, Cao Z, Li W, Chen Z, Wu Y. Plectasin, first animal toxin-like fungal defensin blocking potassium channels through recognizing channel pore region. Toxins (Basel). 2015 Jan 5;7(1):34-42. doi: 10.3390/toxins7010034. PMID:25568977 doi:http://dx.doi.org/10.3390/toxins7010034
  3. ↑ Mandal K, Pentelute BL, Tereshko V, Thammavongsa V, Schneewind O, Kossiakoff AA, Kent SB. Racemic crystallography of synthetic protein enantiomers used to determine the X-ray structure of plectasin by direct methods. Protein Sci. 2009 Jun;18(6):1146-54. PMID:19472324 doi:10.1002/pro.127

3e7r, resolution 1.00Å

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