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== | ==Crystal structure of the complex of peptidyl-tRNA hydrolase from Acinetobacter baumannii with cytidine at 1.87 A resolution== | ||
[[4jwk]] is a 1 chain structure with sequence from [ | <StructureSection load='4jwk' size='340' side='right'caption='[[4jwk]], [[Resolution|resolution]] 1.87Å' scene=''> | ||
[[ | == Structural highlights == | ||
[[ | <table><tr><td colspan='2'>[[4jwk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Acinetobacter_baumannii_ATCC_19606_=_CIP_70.34_=_JCM_6841 Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JWK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JWK FirstGlance]. <br> | ||
[[ | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.87Å</td></tr> | ||
[[ | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CTN:4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE'>CTN</scene></td></tr> | ||
[[Category: | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4jwk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jwk OCA], [https://pdbe.org/4jwk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jwk RCSB], [https://www.ebi.ac.uk/pdbsum/4jwk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jwk ProSAT]</span></td></tr> | ||
[[Category: | </table> | ||
[[Category: | == Function == | ||
[[Category: | [https://www.uniprot.org/uniprot/D0C9L6_ACIB2 D0C9L6_ACIB2] The natural substrate for this enzyme may be peptidyl-tRNAs which drop off the ribosome during protein synthesis.[HAMAP-Rule:MF_00083] | ||
[[Category: | <div style="background-color:#fffaf0;"> | ||
[[Category: | == Publication Abstract from PubMed == | ||
[[Category: | The incidences of infections caused by an aerobic Gram-negative bacterium, Acinetobacter baumannii are very common in hospital environments. It usually causes soft tissue infections including urinary tract infections and pneumonia. It is difficult to treat due to acquired resistance to available antibiotics is well known. In order to design specific inhibitors against one of the important enzymes, peptidyl-tRNA hydrolase from Acinetobacter baumannii, we have determined its three-dimensional structure. Peptidyl-tRNA hydrolase (AbPth) is involved in recycling of peptidyl-tRNAs which are produced in the cell as a result of premature termination of translation process. We have also determined the structures of two complexes of AbPth with cytidine and uridine. AbPth was cloned, expressed and crystallized in unbound and in two bound states with cytidine and uridine. The binding studies carried out using fluorescence spectroscopic and surface plasmon resonance techniques revealed that both cytidine and uridine bound to AbPth at nanomolar concentrations. The structure determinations of the complexes revealed that both ligands were located in the active site cleft of AbPth. The introduction of ligands to AbPth caused a significant widening of the entrance gate to the active site region and in the process of binding, it expelled several water molecules from the active site. As a result of interactions with protein atoms, the ligands caused conformational changes in several residues to attain the induced tight fittings. Such a binding capability of this protein makes it a versatile molecule for hydrolysis of peptidyl-tRNAs having variable peptide sequences. These are the first studies that revealed the mode of inhibitor binding in Peptidyl-tRNA hydrolases which will facilitate the structure based ligand design. | ||
[[Category: | |||
[[Category: | The Mode of Inhibitor Binding to Peptidyl-tRNA Hydrolase: Binding Studies and Structure Determination of Unbound and Bound Peptidyl-tRNA Hydrolase from Acinetobacter baumannii.,Kaushik S, Singh N, Yamini S, Singh A, Sinha M, Arora A, Kaur P, Sharma S, Singh TP PLoS One. 2013 Jul 3;8(7):e67547. doi: 10.1371/journal.pone.0067547. Print 2013. PMID:23844024<ref>PMID:23844024</ref> | ||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4jwk" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Peptidyl-tRNA hydrolase|Peptidyl-tRNA hydrolase]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Acinetobacter baumannii ATCC 19606 = CIP 70 34 = JCM 6841]] | |||
[[Category: Large Structures]] | |||
[[Category: Kaur P]] | |||
[[Category: Kaushik S]] | |||
[[Category: Sharma S]] | |||
[[Category: Singh A]] | |||
[[Category: Singh N]] | |||
[[Category: Singh TP]] | |||
[[Category: Sinha M]] | |||
[[Category: Yamini S]] | |||
Latest revision as of 17:26, 8 November 2023
Crystal structure of the complex of peptidyl-tRNA hydrolase from Acinetobacter baumannii with cytidine at 1.87 A resolutionCrystal structure of the complex of peptidyl-tRNA hydrolase from Acinetobacter baumannii with cytidine at 1.87 A resolution
Structural highlights
FunctionD0C9L6_ACIB2 The natural substrate for this enzyme may be peptidyl-tRNAs which drop off the ribosome during protein synthesis.[HAMAP-Rule:MF_00083] Publication Abstract from PubMedThe incidences of infections caused by an aerobic Gram-negative bacterium, Acinetobacter baumannii are very common in hospital environments. It usually causes soft tissue infections including urinary tract infections and pneumonia. It is difficult to treat due to acquired resistance to available antibiotics is well known. In order to design specific inhibitors against one of the important enzymes, peptidyl-tRNA hydrolase from Acinetobacter baumannii, we have determined its three-dimensional structure. Peptidyl-tRNA hydrolase (AbPth) is involved in recycling of peptidyl-tRNAs which are produced in the cell as a result of premature termination of translation process. We have also determined the structures of two complexes of AbPth with cytidine and uridine. AbPth was cloned, expressed and crystallized in unbound and in two bound states with cytidine and uridine. The binding studies carried out using fluorescence spectroscopic and surface plasmon resonance techniques revealed that both cytidine and uridine bound to AbPth at nanomolar concentrations. The structure determinations of the complexes revealed that both ligands were located in the active site cleft of AbPth. The introduction of ligands to AbPth caused a significant widening of the entrance gate to the active site region and in the process of binding, it expelled several water molecules from the active site. As a result of interactions with protein atoms, the ligands caused conformational changes in several residues to attain the induced tight fittings. Such a binding capability of this protein makes it a versatile molecule for hydrolysis of peptidyl-tRNAs having variable peptide sequences. These are the first studies that revealed the mode of inhibitor binding in Peptidyl-tRNA hydrolases which will facilitate the structure based ligand design. The Mode of Inhibitor Binding to Peptidyl-tRNA Hydrolase: Binding Studies and Structure Determination of Unbound and Bound Peptidyl-tRNA Hydrolase from Acinetobacter baumannii.,Kaushik S, Singh N, Yamini S, Singh A, Sinha M, Arora A, Kaur P, Sharma S, Singh TP PLoS One. 2013 Jul 3;8(7):e67547. doi: 10.1371/journal.pone.0067547. Print 2013. PMID:23844024[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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