1g63: Difference between revisions

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<StructureSection load='1g63' size='340' side='right'caption='[[1g63]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
<StructureSection load='1g63' size='340' side='right'caption='[[1g63]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1g63]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/"albococcus_epidermidis"_winslow_and_winslow_1908 "albococcus epidermidis" winslow and winslow 1908]. 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 [http://proteopedia.org/fgij/fg.htm?mol=1G63 FirstGlance]. <br>
<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>
</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>
</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1g5q|1g5q]]</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>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">EPID ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1282 "Albococcus epidermidis" Winslow and Winslow 1908])</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=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>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1g63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g63 OCA], [http://pdbe.org/1g63 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1g63 RCSB], [http://www.ebi.ac.uk/pdbsum/1g63 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1g63 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://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.  
[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 ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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].
</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>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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:11101502<ref>PMID:11101502</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1g63" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Albococcus epidermidis winslow and winslow 1908]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Blaesse, M]]
[[Category: Staphylococcus epidermidis]]
[[Category: Huber, R]]
[[Category: Blaesse M]]
[[Category: Kupke, T]]
[[Category: Huber R]]
[[Category: Steinbac, S]]
[[Category: Kupke T]]
[[Category: Alpha]]
[[Category: Steinbac S]]
[[Category: Beta protein]]
[[Category: Oxidoreductase]]
[[Category: Rossmann like fold]]

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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OCA
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