5ZK0

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

• PDB DOI: https://doi.org/10.2210/pdb5ZK0/pdb
• Entry: 5ZK0 supersedes: 5H6F

• Classification: HYDROLASE
• Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-03-22 Released: 2018-06-06 
• Deposition Author(s): Shahid, S., Kabra, A., Pal, R.K., Arora, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.263 
• R-Value Work: 0.186 
• R-Value Observed: 0.190 

Literature

Role of methionine 71 in substrate recognition and structural integrity of bacterial peptidyl-tRNA hydrolase.

Shahid, S., Kabra, A., Mundra, S., Pal, R.K., Tripathi, S., Jain, A., Arora, A.

(2018) Biochim Biophys Acta 1866: 865-874

• PubMed: 29733913 
• DOI: https://doi.org/10.1016/j.bbapap.2018.05.002
• Primary Citation of Related Structures:  
  5ZK0


• PubMed Abstract: 
  

  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.

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Organizational Affiliation: 

Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 43.48 kDa 
• Atom Count: 3,061 
• Modelled Residue Count: 390 
• Deposited Residue Count: 398 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-tRNA hydrolase	A, B	199	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 1  Gene Names: pth, VC_2184 EC: 3.1.1.29
UniProt
Find proteins for Q9KQ21 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KQ21  Go to UniProtKB:  Q9KQ21

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	C [auth A], D [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
2CO	A, B	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.263 
• R-Value Work: 0.186 
• R-Value Observed: 0.190 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.709	α = 90
b = 117.491	β = 90
c = 201.618	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-06-06 
Deposition Author(s): Shahid, S., Kabra, A., Pal, R.K., Arora, A.
• This entry supersedes: 5H6F

Revision History  

• Version 1.0: 2018-06-06
  Type: Initial release
  
• Version 1.1: 2018-06-20
  Changes: Data collection, Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description