This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
3eef
From Proteopedia
(Difference between revisions)
m (Protected "3eef" [edit=sysop:move=sysop]) |
|||
| Line 1: | Line 1: | ||
| - | [[ | + | ==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 [http://en.wikipedia.org/wiki/Thermoplasma_acidophilum Thermoplasma acidophilum]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EEF FirstGlance]. <br> | ||
| + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2303 Thermoplasma acidophilum])</td></tr> | ||
| + | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N-carbamoylsarcosine_amidase N-carbamoylsarcosine amidase], with EC number [http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3eef FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eef OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3eef RCSB], [http://www.ebi.ac.uk/pdbsum/3eef PDBsum], [http://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/chain_selection.php?pdb_ID=2ata 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> | |
| - | + | == References == | |
| - | + | <references/> | |
| - | + | __TOC__ | |
| - | + | </StructureSection> | |
| - | + | ||
| - | == | + | |
| - | < | + | |
[[Category: N-carbamoylsarcosine amidase]] | [[Category: N-carbamoylsarcosine amidase]] | ||
[[Category: Thermoplasma acidophilum]] | [[Category: Thermoplasma acidophilum]] | ||
| - | [[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: | + | [[Category: Structural genomic]] |
| - | [[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]] |
| - | + | ||
| - | + | ||
Revision as of 13:35, 19 November 2014
Crystal structure of N-carbamoylsarcosine amidase from thermoplasma acidophilum
| |||||||||||
