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3eef
From Proteopedia
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| - | [[Image:3eef.png|left|200px]] | ||
| - | + | ==Crystal structure of N-carbamoylsarcosine amidase from thermoplasma acidophilum== | |
| + | <StructureSection load='3eef' size='340' side='right'caption='[[3eef]], [[Resolution|resolution]] 2.35Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[3eef]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"thermoplasma_acidophila"_(sic)_darland_et_al._1970 "thermoplasma acidophila" (sic) darland et al. 1970]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EEF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EEF FirstGlance]. <br> | ||
| + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Ta0454 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2303 "Thermoplasma acidophila" (sic) Darland et al. 1970])</td></tr> | ||
| + | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/N-carbamoylsarcosine_amidase N-carbamoylsarcosine amidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.59 3.5.1.59] </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=3eef FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eef OCA], [https://pdbe.org/3eef PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3eef RCSB], [https://www.ebi.ac.uk/pdbsum/3eef PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3eef ProSAT], [https://www.topsan.org/Proteins/MCSG/3eef TOPSAN]</span></td></tr> | ||
| + | </table> | ||
| + | == 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/ee/3eef_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=3eef ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | A crystal structure of the putative N-carbamoylsarcosine amidase (CSHase) Ta0454 from Thermoplasma acidophilum was solved by single-wavelength anomalous diffraction and refined at a resolution of 2.35A. CSHases are involved in the degradation of creatinine. Ta0454 shares a similar fold and a highly conserved C-D-K catalytic triad (Cys123, Asp9, and Lys90) with the structures of three cysteine hydrolases (PDB codes 1NBA, 1IM5, and 2H0R). Molecular dynamics (MD) simulations of Ta0454/N-carbamoylsarcosine and Ta0454/pyrazinamide complexes were performed to determine the structural basis of the substrate binding pattern for each ligand. Based on the MD-simulated trajectories, the MM/PBSA method predicts binding free energies of -24.5 and -17.1 kcal/mol for the two systems, respectively. The predicted binding free energies suggest that Ta0454 is selective for N-carbamoylsarcosine over pyrazinamide, and zinc ions play an important role in the favorable substrate bound states. | ||
| - | + | Crystal structure and molecular modeling study of N-carbamoylsarcosine amidase Ta0454 from Thermoplasma acidophilum.,Luo HB, Zheng H, Zimmerman MD, Chruszcz M, Skarina T, Egorova O, Savchenko A, Edwards AM, Minor W J Struct Biol. 2010 Mar;169(3):304-11. Epub 2009 Nov 20. PMID:19932181<ref>PMID:19932181</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | + | <div class="pdbe-citations 3eef" style="background-color:#fffaf0;"></div> | |
| - | + | == References == | |
| - | + | <references/> | |
| - | == | + | __TOC__ |
| - | < | + | </StructureSection> |
| + | [[Category: Large Structures]] | ||
[[Category: N-carbamoylsarcosine amidase]] | [[Category: N-carbamoylsarcosine amidase]] | ||
| - | + | [[Category: Chruszcz, M]] | |
| - | [[Category: Chruszcz, M | + | [[Category: Egorova, O]] |
| - | [[Category: Egorova, O | + | [[Category: Joachimiak, A]] |
| - | [[Category: Joachimiak, A | + | [[Category: Luo, H B]] |
| - | [[Category: Luo, H B | + | [[Category: Structural genomic]] |
| - | [[Category: | + | [[Category: Minor, W]] |
| - | [[Category: Minor, W | + | [[Category: Savchenko, A]] |
| - | [[Category: Savchenko, A | + | [[Category: Skarina, T]] |
| - | [[Category: Skarina, T | + | [[Category: Zheng, H]] |
| - | [[Category: Zheng, H | + | [[Category: Zimmerman, M D]] |
| - | [[Category: Zimmerman, M D | + | |
[[Category: Hydrolase]] | [[Category: Hydrolase]] | ||
[[Category: Mcsg]] | [[Category: Mcsg]] | ||
| - | [[Category: Midwest center for structural genomic]] | ||
| - | [[Category: N-carbamoylsarcosine amidase]] | ||
[[Category: Protein]] | [[Category: Protein]] | ||
| - | [[Category: Protein structure initiative | + | [[Category: PSI, Protein structure initiative]] |
| - | + | ||
| - | + | ||
Current revision
Crystal structure of N-carbamoylsarcosine amidase from thermoplasma acidophilum
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