1g63: Difference between revisions

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New page: left|200px<br /><applet load="1g63" size="450" color="white" frame="true" align="right" spinBox="true" caption="1g63, resolution 2.50Å" /> '''PEPTIDYL-CYSTEINE DE...
 
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[[Image:1g63.gif|left|200px]]<br /><applet load="1g63" size="450" color="white" frame="true" align="right" spinBox="true"
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'''PEPTIDYL-CYSTEINE DECARBOXYLASE EPID'''<br />


==Overview==
==PEPTIDYL-CYSTEINE DECARBOXYLASE EPID==
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='1g63' size='340' side='right'caption='[[1g63]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[1g63]] is a 12 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=1G63 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1G63 FirstGlance]. <br>
1G63 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Staphylococcus_epidermidis Staphylococcus epidermidis] with FMN as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1G63 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]] 2.5&#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></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=1g63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g63 OCA], [https://pdbe.org/1g63 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1g63 RCSB], [https://www.ebi.ac.uk/pdbsum/1g63 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1g63 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: Single protein]]
== 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/g6/1g63_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=1g63 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: Steinbac, S.]]
[[Category: Steinbac S]]
[[Category: FMN]]
[[Category: alpha]]
[[Category: beta protein]]
[[Category: rossmann like fold]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 15:44:22 2007''

Latest revision as of 10:23, 7 February 2024

PEPTIDYL-CYSTEINE DECARBOXYLASE EPIDPEPTIDYL-CYSTEINE DECARBOXYLASE EPID

Structural highlights

1g63 is a 12 chain structure with sequence from Staphylococcus epidermidis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.5Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

1g63, resolution 2.50Å

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