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5zk0

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Revision as of 06:21, 20 June 2018

Crystal structure of Peptidyl-tRNA hydrolase mutant -M71A from Vibrio cholerae

Structural highlights

5zk0 is a 2 chain structure with sequence from Vibch. This structure supersedes the now removed PDB entry 5h6f. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
NonStd Res:
Gene:	pth, VC_2184 (VIBCH)
Activity:	Aminoacyl-tRNA hydrolase, with EC number 3.1.1.29
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[PTH_VIBCH] The natural substrate for this enzyme may be peptidyl-tRNAs which drop off the ribosome during protein synthesis.

Publication Abstract from PubMed

BACKGROUND: Bacterial peptidyl-tRNA hydrolase (Pth) is an essential enzyme that alleviates tRNA starvation by recycling prematurely dissociated peptidyl-tRNAs. The specificity of Pth for N-blocked-aminoacyl-tRNA has been proposed to be contingent upon conserved residue N14 forming a hydrogen bond with the carbonyl of the first peptide bond in the substrate. M71 is involved in forming a conserved hydrogen bond with N14. Other interactions facilitating this recognition are not known. METHODS: The structure, dynamics, and stability of the M71A mutant of Pth from Vibrio cholerae (VcPth) were characterized by X-ray crystallography, NMR spectroscopy, MD simulations and DSC. RESULTS: Crystal structure of M71A mutant was determined. In the structure, the dimer interface is formed by the insertion of six C-terminal residues of one molecule into the active site of another molecule. The side-chain amide of N14 was hydrogen bonded to the carbonyl of the last peptide bond formed between residues A196 and E197, and also to A71. The CSP profile of mutation was similar to that observed for the N14D mutant. M71A mutation lowered the thermal stability of the protein. CONCLUSION: Our results indicate that the interactions of M71 with N14 and H24 play an important role in optimal positioning of their side-chains relative to the peptidyl-tRNA substrate. Overall, these interactions of M71 are important for the activity, stability, and compactness of the protein. SIGNIFICANCE: The work presented provides original and new structural and dynamics information that significantly enhances our understanding of the network of interactions that govern this enzyme's activity and selectivity.

Role of methionine 71 in substrate recognition and structural integrity of bacterial peptidyl-tRNA hydrolase.,Shahid S, Kabra A, Mundra S, Pal RK, Tripathi S, Jain A, Arora A Biochim Biophys Acta. 2018 May 5. pii: S1570-9639(18)30067-0. doi:, 10.1016/j.bbapap.2018.05.002. PMID:29733913^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Shahid S, Kabra A, Mundra S, Pal RK, Tripathi S, Jain A, Arora A. Role of methionine 71 in substrate recognition and structural integrity of bacterial peptidyl-tRNA hydrolase. Biochim Biophys Acta. 2018 May 5. pii: S1570-9639(18)30067-0. doi:, 10.1016/j.bbapap.2018.05.002. PMID:29733913 doi:http://dx.doi.org/10.1016/j.bbapap.2018.05.002

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5zk0"

@@ Line 3: / Line 3: @@
 <StructureSection load='5zk0' size='340' side='right' caption='[[5zk0]], [[Resolution|resolution]] 2.55&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5zk0]] is a 2 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5h6f 5h6f]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZK0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZK0 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5zk0]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Vibch Vibch]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5h6f 5h6f]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZK0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZK0 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2CO:S-HYDROPEROXYCYSTEINE'>2CO</scene></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pth, VC_2184 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243277 VIBCH])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aminoacyl-tRNA_hydrolase Aminoacyl-tRNA hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.29 3.1.1.29] </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=5zk0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zk0 OCA], [http://pdbe.org/5zk0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zk0 RCSB], [http://www.ebi.ac.uk/pdbsum/5zk0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zk0 ProSAT]</span></td></tr>
@@ Line 28: / Line 29: @@
 </StructureSection>
 [[Category: Aminoacyl-tRNA hydrolase]]
+[[Category: Vibch]]
 [[Category: Arora, A]]
 [[Category: Kabra, A]]

5zk0

From Proteopedia

Revision as of 06:21, 20 June 2018

Crystal structure of Peptidyl-tRNA hydrolase mutant -M71A from Vibrio cholerae

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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