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| | <StructureSection load='1y7m' size='340' side='right'caption='[[1y7m]], [[Resolution|resolution]] 2.05Å' scene=''> | | <StructureSection load='1y7m' size='340' side='right'caption='[[1y7m]], [[Resolution|resolution]] 2.05Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1y7m]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacsu Bacsu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y7M OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1Y7M FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1y7m]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y7M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y7M FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.05Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ykud ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</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=1y7m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y7m OCA], [https://pdbe.org/1y7m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y7m RCSB], [https://www.ebi.ac.uk/pdbsum/1y7m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y7m ProSAT], [https://www.topsan.org/Proteins/MCSG/1y7m TOPSAN]</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=1y7m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y7m OCA], [http://pdbe.org/1y7m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1y7m RCSB], [http://www.ebi.ac.uk/pdbsum/1y7m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1y7m ProSAT], [http://www.topsan.org/Proteins/MCSG/1y7m TOPSAN]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/YKUD_BACSU YKUD_BACSU]] Probable enzyme that may play an important role in cell wall biology.<ref>PMID:16287140</ref> | + | [https://www.uniprot.org/uniprot/YKUD_BACSU YKUD_BACSU] Probable enzyme that may play an important role in cell wall biology.<ref>PMID:16287140</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/y7/1y7m_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/y7/1y7m_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacsu]] | + | [[Category: Bacillus subtilis subsp. subtilis str. 168]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Bielnicki, J A]] | + | [[Category: Bielnicki JA]] |
| - | [[Category: Dauter, Z]] | + | [[Category: Dauter Z]] |
| - | [[Category: Derewenda, U]] | + | [[Category: Derewenda U]] |
| - | [[Category: Derewenda, Z S]] | + | [[Category: Derewenda ZS]] |
| - | [[Category: Devedjiev, Y]] | + | [[Category: Devedjiev Y]] |
| - | [[Category: Joachimiak, A]] | + | [[Category: Joachimiak A]] |
| - | [[Category: Structural genomic]]
| + | |
| - | [[Category: Cell wall catabolism]]
| + | |
| - | [[Category: Cysteine protease]]
| + | |
| - | [[Category: Mcsg]]
| + | |
| - | [[Category: PSI, Protein structure initiative]]
| + | |
| - | [[Category: Surface mutagenesis]]
| + | |
| - | [[Category: Unknown function]]
| + | |
| Structural highlights
Function
YKUD_BACSU Probable enzyme that may play an important role in cell wall biology.[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 PubMed
The crystal structure of the product of the Bacillus subtilis ykuD gene was solved by the multiwavelength anomalous dispersion (MAD) method and refined using data to 2.0 A resolution. The ykuD protein is a representative of a distinctly prokaryotic and ubiquitous family found among both pathogenic and nonpathogenic Gram-positive and Gram-negative bacteria. The deduced amino acid sequence reveals the presence of an N-terminal LysM domain, which occurs among enzymes involved in cell wall metabolism, and a novel, putative catalytic domain with a highly conserved His/Cys-containing motif of hitherto unknown structure. As the wild-type protein did not crystallize, a double mutant was designed (Lys117Ala/Gln118Ala) to reduce excess surface conformational entropy. As expected, the structure of the LysM domain is similar to the NMR structure reported for an analogous domain from Escherichia coli murein transglycosylase MltD. The molecular model also shows that the 112-residue-long C-terminal domain has a novel tertiary fold consisting of a beta-sandwich with two mixed sheets, one containing five strands and the other, six strands. The two beta-sheets form a cradle capped by an alpha-helix. This domain contains a putative catalytic site with a tetrad of invariant His123, Gly124, Cys139, and Arg141. The stereochemistry of this active site shows similarities to peptidotransferases and sortases, and suggests that the enzymes of the ykuD family may play an important role in cell wall biology.
B. subtilis ykuD protein at 2.0 A resolution: insights into the structure and function of a novel, ubiquitous family of bacterial enzymes.,Bielnicki J, Devedjiev Y, Derewenda U, Dauter Z, Joachimiak A, Derewenda ZS Proteins. 2006 Jan 1;62(1):144-51. PMID:16287140[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Bielnicki J, Devedjiev Y, Derewenda U, Dauter Z, Joachimiak A, Derewenda ZS. B. subtilis ykuD protein at 2.0 A resolution: insights into the structure and function of a novel, ubiquitous family of bacterial enzymes. Proteins. 2006 Jan 1;62(1):144-51. PMID:16287140 doi:10.1002/prot.20702
- ↑ Bielnicki J, Devedjiev Y, Derewenda U, Dauter Z, Joachimiak A, Derewenda ZS. B. subtilis ykuD protein at 2.0 A resolution: insights into the structure and function of a novel, ubiquitous family of bacterial enzymes. Proteins. 2006 Jan 1;62(1):144-51. PMID:16287140 doi:10.1002/prot.20702
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