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< | ==Crystal structure of N-carbamoylsarcosine amidase from thermoplasma acidophilum== | ||
<StructureSection load='3eef' size='340' side='right'caption='[[3eef]], [[Resolution|resolution]] 2.35Å' scene=''> | |||
You may | == 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 | |||
[[Category: Hydrolase]] | [[Category: Hydrolase]] | ||
[[Category: Mcsg]] | [[Category: Mcsg]] | ||
[[Category: Protein]] | [[Category: Protein]] | ||
[[Category: Protein structure initiative]] | [[Category: PSI, Protein structure initiative]] | ||
Latest revision as of 14:47, 16 February 2022
Crystal structure of N-carbamoylsarcosine amidase from thermoplasma acidophilumCrystal structure of N-carbamoylsarcosine amidase from thermoplasma acidophilum
Structural highlights
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 PubMedA 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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