1g5q: Difference between revisions

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[[Image:1g5q.jpg|left|200px]]<br /><applet load="1g5q" size="350" color="white" frame="true" align="right" spinBox="true"
caption="1g5q, resolution 2.57&Aring;" />
'''EPID H67N COMPLEXED WITH SUBSTRATE PEPTIDE DSYTC'''<br />


==Overview==
==EPID H67N COMPLEXED WITH SUBSTRATE PEPTIDE DSYTC==
Epidermin from Staphylococcus epidermidis Tu3298 is an antimicrobial peptide of the lantibiotic family that contains, amongst other unusual amino acids, S:-[(Z:)- 2-aminovinyl]-D-cysteine. This residue is introduced by post-translational modification of the ribosomally synthesized precursor EpiA. Modification starts with the oxidative decarboxylation of its C-terminal cysteine by the flavoprotein EpiD generating a reactive (Z:)-enethiol intermediate. We have determined the crystal structures of EpiD and EpiD H67N in complex with the substrate pentapeptide DSYTC at 2.5 A resolution. Rossmann-type monomers build up a dodecamer of 23 point symmetry with trimers disposed at the vertices of a tetrahedron. Oligomer formation is essential for binding of flavin mononucleotide and substrate, which is buried by an otherwise disordered substrate recognition clamp. A pocket for the tyrosine residue of the substrate peptide is formed by an induced fit mechanism. The substrate contacts flavin mononucleotide only via Cys-Sgamma, suggesting its oxidation as the initial step. A thioaldehyde intermediate could undergo spontaneous decarboxylation. The unusual substrate recognition mode and the type of chemical reaction performed provide insight into a novel family of flavoproteins.
<StructureSection load='1g5q' size='340' side='right'caption='[[1g5q]], [[Resolution|resolution]] 2.57&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[1g5q]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_epidermidis Staphylococcus epidermidis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G5Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1G5Q FirstGlance]. <br>
1G5Q is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Staphylococcus_epidermidis Staphylococcus epidermidis] with <scene name='pdbligand=FMN:'>FMN</scene> and <scene name='pdbligand=TRS:'>TRS</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G5Q OCA].  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.57&#8491;</td></tr>
 
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
==Reference==
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1g5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g5q OCA], [https://pdbe.org/1g5q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1g5q RCSB], [https://www.ebi.ac.uk/pdbsum/1g5q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1g5q ProSAT]</span></td></tr>
Crystal structure of the peptidyl-cysteine decarboxylase EpiD complexed with a pentapeptide substrate., Blaesse M, Kupke T, Huber R, Steinbacher S, EMBO J. 2000 Dec 1;19(23):6299-310. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11101502 11101502]
</table>
[[Category: Protein complex]]
== Function ==
[https://www.uniprot.org/uniprot/EPID_STAEP EPID_STAEP] Catalyzes the removal of two reducing equivalents (oxidative decarboxylation) from the cysteine residue of the C-terminal meso-lanthionine of epidermin to form a --C==C-- double bond.
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g5/1g5q_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1g5q ConSurf].
<div style="clear:both"></div>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Staphylococcus epidermidis]]
[[Category: Staphylococcus epidermidis]]
[[Category: Blaesse, M.]]
[[Category: Blaesse M]]
[[Category: Huber, R.]]
[[Category: Huber R]]
[[Category: Kupke, T.]]
[[Category: Kupke T]]
[[Category: Steinbacher, S.]]
[[Category: Steinbacher S]]
[[Category: FMN]]
[[Category: TRS]]
[[Category: alpha]]
[[Category: beta protein]]
[[Category: rossman like fold]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:46:26 2008''

Latest revision as of 07:23, 7 February 2024

EPID H67N COMPLEXED WITH SUBSTRATE PEPTIDE DSYTC

1g5q, resolution 2.57Å

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