1p3y: Difference between revisions
New page: left|200px<br /><applet load="1p3y" size="450" color="white" frame="true" align="right" spinBox="true" caption="1p3y, resolution 2.54Å" /> '''MrsD from Bacillus s... |
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== | ==MrsD from Bacillus sp. HIL-Y85/54728== | ||
MrsD from Bacillus sp. HIL-Y85/54728 is a member of the HFCD | <StructureSection load='1p3y' size='340' side='right'caption='[[1p3y]], [[Resolution|resolution]] 2.54Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1p3y]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp._HIL-Y85/54728 Bacillus sp. HIL-Y85/54728]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P3Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1P3Y FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.54Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></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=1p3y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p3y OCA], [https://pdbe.org/1p3y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1p3y RCSB], [https://www.ebi.ac.uk/pdbsum/1p3y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1p3y ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/MRSD_BACSY MRSD_BACSY] Catalyzes the oxidative decarboxylation of the C-terminal cysteine residue of mersacidin to an aminoenethiol residue.<ref>PMID:11844751</ref> | |||
== 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/p3/1p3y_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=1p3y ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
MrsD from Bacillus sp. HIL-Y85/54728 is a member of the HFCD (homo-oligomeric flavin-containing Cys decarboxylases) family of flavoproteins and is involved in the biosynthesis of the lantibiotic mersacidin. It catalyses the oxidative decarboxylation of the C-terminal cysteine residue of the MrsA precursor peptide of mersacidin, yielding a (Z)-enethiol intermediate as the first step in the formation of the unusual amino acid S-[(Z)-2-aminovinyl]-methyl-D-cysteine. Surprisingly, MrsD was found to bind FAD, in contrast to the three other characterized members of the HFCD family, which bind FMN. To determine the molecular discriminators of FAD binding within the HFCD family, the crystal structure of MrsD was analyzed at a resolution of 2.54 A. Crystals of space group F432 contain one MrsD monomer in the asymmetric unit. However, a Patterson search with EpiD-derived models failed. Based on the consideration that the dodecameric MrsD particle of tetrahedral symmetry resembles the quaternary structure of EpiD, rotational and translational parameters were derived from the geometric consideration that the MrsD dodecamer is generated from a monomer by crystallographic symmetry around the position (1/4, 1/4, 1/4) of the unit cell. A structural comparison with the FMN-binding members of the HFCD family EpiD and AtHAL3a shows conserved sequence motifs in contact with the flavin's pyrimidine ring but divergent environments for the dimethylbenzene ring of the isoalloxazine moiety. The position of the ribityl chain differs in MrsD from that found in EpiD and AtHAL3a. However, the FMN-phosphate binding sites are also highly conserved in their exact positions. In all three cases, the flavin cofactor is bound to a structurally conserved region of the Rossmann-fold monomer, exposing its Re side for catalysis. The adenosyl phosphate of FAD is anchored in a well defined binding site and the adenosine moieties are oriented towards the interior of the hollow particle, where three of them pack against each other around the threefold axis of a trimeric facet. | |||
Structure of MrsD, an FAD-binding protein of the HFCD family.,Blaesse M, Kupke T, Huber R, Steinbacher S Acta Crystallogr D Biol Crystallogr. 2003 Aug;59(Pt 8):1414-21. Epub 2003, Jul 23. PMID:12876343<ref>PMID:12876343</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
[[Category: Bacillus sp.]] | <div class="pdbe-citations 1p3y" style="background-color:#fffaf0;"></div> | ||
[[Category: | == References == | ||
[[Category: Blaesse | <references/> | ||
[[Category: Huber | __TOC__ | ||
[[Category: Kupke | </StructureSection> | ||
[[Category: Steinbacher | [[Category: Bacillus sp. HIL-Y85/54728]] | ||
[[Category: Large Structures]] | |||
[[Category: Blaesse M]] | |||
[[Category: Huber R]] | |||
[[Category: Kupke T]] | |||
[[Category: Steinbacher S]] | |||
Latest revision as of 10:22, 25 October 2023
MrsD from Bacillus sp. HIL-Y85/54728MrsD from Bacillus sp. HIL-Y85/54728
Structural highlights
FunctionMRSD_BACSY Catalyzes the oxidative decarboxylation of the C-terminal cysteine residue of mersacidin to an aminoenethiol residue.[1] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedMrsD from Bacillus sp. HIL-Y85/54728 is a member of the HFCD (homo-oligomeric flavin-containing Cys decarboxylases) family of flavoproteins and is involved in the biosynthesis of the lantibiotic mersacidin. It catalyses the oxidative decarboxylation of the C-terminal cysteine residue of the MrsA precursor peptide of mersacidin, yielding a (Z)-enethiol intermediate as the first step in the formation of the unusual amino acid S-[(Z)-2-aminovinyl]-methyl-D-cysteine. Surprisingly, MrsD was found to bind FAD, in contrast to the three other characterized members of the HFCD family, which bind FMN. To determine the molecular discriminators of FAD binding within the HFCD family, the crystal structure of MrsD was analyzed at a resolution of 2.54 A. Crystals of space group F432 contain one MrsD monomer in the asymmetric unit. However, a Patterson search with EpiD-derived models failed. Based on the consideration that the dodecameric MrsD particle of tetrahedral symmetry resembles the quaternary structure of EpiD, rotational and translational parameters were derived from the geometric consideration that the MrsD dodecamer is generated from a monomer by crystallographic symmetry around the position (1/4, 1/4, 1/4) of the unit cell. A structural comparison with the FMN-binding members of the HFCD family EpiD and AtHAL3a shows conserved sequence motifs in contact with the flavin's pyrimidine ring but divergent environments for the dimethylbenzene ring of the isoalloxazine moiety. The position of the ribityl chain differs in MrsD from that found in EpiD and AtHAL3a. However, the FMN-phosphate binding sites are also highly conserved in their exact positions. In all three cases, the flavin cofactor is bound to a structurally conserved region of the Rossmann-fold monomer, exposing its Re side for catalysis. The adenosyl phosphate of FAD is anchored in a well defined binding site and the adenosine moieties are oriented towards the interior of the hollow particle, where three of them pack against each other around the threefold axis of a trimeric facet. Structure of MrsD, an FAD-binding protein of the HFCD family.,Blaesse M, Kupke T, Huber R, Steinbacher S Acta Crystallogr D Biol Crystallogr. 2003 Aug;59(Pt 8):1414-21. Epub 2003, Jul 23. PMID:12876343[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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