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| | <StructureSection load='3v48' size='340' side='right'caption='[[3v48]], [[Resolution|resolution]] 2.10Å' scene=''> | | <StructureSection load='3v48' size='340' side='right'caption='[[3v48]], [[Resolution|resolution]] 2.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3v48]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecose Ecose]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V48 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3V48 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3v48]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_SE11 Escherichia coli SE11]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V48 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3V48 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</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]] 2.1Å</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ECSE_1071, rutD ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=409438 ECOSE])</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=3v48 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v48 OCA], [https://pdbe.org/3v48 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3v48 RCSB], [https://www.ebi.ac.uk/pdbsum/3v48 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3v48 ProSAT]</span></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=3v48 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v48 OCA], [https://pdbe.org/3v48 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3v48 RCSB], [https://www.ebi.ac.uk/pdbsum/3v48 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3v48 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/RUTD_ECOSE RUTD_ECOSE]] May increase the rate of spontaneous hydrolysis of aminoacrylate to malonic semialdehyde. Required to remove a toxic intermediate produce in the pyrimidine nitrogen degradation (By similarity).
| + | [https://www.uniprot.org/uniprot/RUTD_ECOSE RUTD_ECOSE] May increase the rate of spontaneous hydrolysis of aminoacrylate to malonic semialdehyde. Required to remove a toxic intermediate produce in the pyrimidine nitrogen degradation (By similarity). |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Ecose]] | + | [[Category: Escherichia coli SE11]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Almo, S C]] | + | [[Category: Almo SC]] |
| - | [[Category: Chruszcz, M]] | + | [[Category: Chruszcz M]] |
| - | [[Category: Cooper, D R]] | + | [[Category: Cooper DR]] |
| - | [[Category: Cymborowski, M T]] | + | [[Category: Cymborowski MT]] |
| - | [[Category: Knapik, A A]] | + | [[Category: Knapik AA]] |
| - | [[Category: Minor, W]] | + | [[Category: Minor W]] |
| - | [[Category: Structural genomic]]
| + | [[Category: Niedzialkowska E]] |
| - | [[Category: Niedzialkowska, E]] | + | [[Category: Otwinowski Z]] |
| - | [[Category: Otwinowski, Z]] | + | [[Category: Petkowski JJ]] |
| - | [[Category: Petkowski, J J]] | + | [[Category: Porebski PJ]] |
| - | [[Category: Porebski, P J]] | + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Nysgrc]]
| + | |
| - | [[Category: Psi-biology]]
| + | |
| Structural highlights
Function
RUTD_ECOSE May increase the rate of spontaneous hydrolysis of aminoacrylate to malonic semialdehyde. Required to remove a toxic intermediate produce in the pyrimidine nitrogen degradation (By similarity).
Publication Abstract from PubMed
The rut pathway of pyrimidine catabolism is a novel pathway that allows pyrimidine bases to serve as the sole nitrogen source in suboptimal temperatures. The rut operon in E. coli evaded detection until 2006, yet consists of seven proteins named RutA, RutB, etc. through RutG. The operon is comprised of a pyrimidine transporter and six enzymes that cleave and further process the uracil ring. Herein, we report the structure of RutD, a member of the alpha/beta hydrolase superfamily, which is proposed to enhance the rate of hydrolysis of aminoacrylate, a toxic side product of uracil degradation, to malonic semialdehyde. Although this reaction will occur spontaneously in water, the toxicity of aminoacrylate necessitates catalysis by RutD for efficient growth with uracil as a nitrogen source. RutD has a novel and conserved arrangement of residues corresponding to the alpha/beta hydrolase active site, where the nucleophile's spatial position occupied by Ser, Cys or Asp of the canonical catalytic triad is replaced by histidine. We have used a combination of crystallographic structure determination, modeling and bioinformatics, to propose a novel mechanism for this enzyme. This approach also revealed that RutD represents a previously undescribed family within the alpha/beta hydrolases. We compare and contrast RutD with PcaD, which is the closest structural homolog to RutD. PcaD is a 3-oxoadipate-enol-lactonase- with a classic arrangement of residues in the active site. We have modeled a substrate in the PcaD active site and proposed a reaction mechanism. Proteins 2012. (c) 2012 Wiley Periodicals, Inc.
A multi-faceted analysis of RutD reveals a novel family of alpha/beta hydrolases.,Knapik AA, Petkowski JJ, Otwinowski Z, Cymborowski MT, Cooper DR, Majorek KA, Chruszcz M, Krajewska WM, Minor W Proteins. 2012 May 29. doi: 10.1002/prot.24122. PMID:22641504[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Knapik AA, Petkowski JJ, Otwinowski Z, Cymborowski MT, Cooper DR, Majorek KA, Chruszcz M, Krajewska WM, Minor W. A multi-faceted analysis of RutD reveals a novel family of alpha/beta hydrolases. Proteins. 2012 May 29. doi: 10.1002/prot.24122. PMID:22641504 doi:10.1002/prot.24122
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