3kjz
From Proteopedia
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==Crystal structure of native peptidyl-tRNA hydrolase from Mycobacterium smegmatis== | ==Crystal structure of native peptidyl-tRNA hydrolase from Mycobacterium smegmatis== | ||
| - | <StructureSection load='3kjz' size='340' side='right' caption='[[3kjz]], [[Resolution|resolution]] 2.40Å' scene=''> | + | <StructureSection load='3kjz' size='340' side='right'caption='[[3kjz]], [[Resolution|resolution]] 2.40Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[3kjz]] is a 1 chain structure with sequence from [ | + | <table><tr><td colspan='2'>[[3kjz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis_MC2_155 Mycolicibacterium smegmatis MC2 155]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KJZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KJZ FirstGlance]. <br> |
| - | </td></tr><tr id=' | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4Å</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=3kjz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kjz OCA], [https://pdbe.org/3kjz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kjz RCSB], [https://www.ebi.ac.uk/pdbsum/3kjz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kjz ProSAT]</span></td></tr> | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | |
</table> | </table> | ||
== Function == | == Function == | ||
| - | [ | + | [https://www.uniprot.org/uniprot/PTH_MYCS2 PTH_MYCS2] The natural substrate for this enzyme may be peptidyl-tRNAs which drop off the ribosome during protein synthesis (By similarity). |
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kj/3kjz_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kj/3kjz_consurf.spt"</scriptWhenChecked> |
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </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/ | + | </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=3kjz ConSurf]. |
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Peptidyl-tRNA hydrolase from Mycobacterium smegmatis is a single domain 21 kDa protein involved in the hydrolysis of prematurely produced peptidyl-tRNAs to ensure the viability of cells in bacteria, thus making it a potentially important drug target. In order to aid the development of potent drugs for controlling bacterial infections, the three-dimensional structure of peptidyl-tRNA hydrolase from Mycobacterium smegmatis has been determined. The protein adopts a compact alpha/beta globular fold with a twisted beta-sheet surrounded by alpha-helices. The functionally important C-terminal stretch has been unambiguously modeled for the first time in the unliganded structure of peptidyl-tRNA hydrolase. The segment, Gly138 - Val150 is mobile because it lacks significant interactions with the rest of the protein molecule. This conformational flexibility is reflected through different values of distances between a reference atom Ala147 C(alpha) of the segment Gly138 - Val150 to Gly114 C(alpha) from another segment from opposite side of the substrate binding channel in Mycobacterium smegmatis (7.8 A), Mycobacterium tuberculosis (9.5 A) and Escherichia coli (11.8 A). Similarly, the conformation of loop Gly109 - Gly117 with respect to another loop Asp95 - Asp100 also shows variability of the substrate binding cleft as the distance between Asp98 O(delta2) to Gly113 C(alpha) in Mycobacterium smegmatis is 4.5 A while the corresponding distances in Mycobacterium tuberculosis and Escherichia coli are 3.1 A and 6.7 A respectively. The hydrogen bonded interactions between Asn116, His22 and Asp95 indicate a stereochemically favorable arrangement of these residues for catalytic action. | ||
| + | |||
| + | Crystal structure of peptidyl-tRNA hydrolase from mycobacterium smegmatis reveals novel features related to enzyme dynamics.,Kumar A, Singh N, Yadav R, Kumar RP, Sharma S, Arora A, Singh TP Int J Biochem Mol Biol. 2012;3(1):58-69. Epub 2012 Feb 15. PMID:22509481<ref>PMID:22509481</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 3kjz" style="background-color:#fffaf0;"></div> | ||
==See Also== | ==See Also== | ||
*[[Peptidyl-tRNA hydrolase|Peptidyl-tRNA hydrolase]] | *[[Peptidyl-tRNA hydrolase|Peptidyl-tRNA hydrolase]] | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| - | [[Category: | + | [[Category: Large Structures]] |
| - | [[Category: | + | [[Category: Mycolicibacterium smegmatis MC2 155]] |
| - | [[Category: Arora | + | [[Category: Arora A]] |
| - | [[Category: Kumar | + | [[Category: Kumar A]] |
| - | [[Category: Kumar | + | [[Category: Prem Kumar R]] |
| - | [[Category: Sharma | + | [[Category: Sharma S]] |
| - | [[Category: Singh | + | [[Category: Singh N]] |
| - | [[Category: Singh | + | [[Category: Singh TP]] |
| - | [[Category: Yadav | + | [[Category: Yadav R]] |
| - | + | ||
| - | + | ||
Current revision
Crystal structure of native peptidyl-tRNA hydrolase from Mycobacterium smegmatis
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