3KJZ

Crystal structure of native peptidyl-tRNA hydrolase from Mycobacterium smegmatis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of peptidyl-tRNA hydrolase from mycobacterium smegmatis reveals novel features related to enzyme dynamics.

Kumar, A.Singh, N.Yadav, R.Kumar, R.P.Sharma, S.Arora, A.Singh, T.P.

(2012) Int J Biochem Mol Biol 3: 58-69

  • Primary Citation of Related Structures:  
    3KJZ

  • PubMed Abstract: 

    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 α/β globular fold with a twisted β-sheet surrounded by α-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(α) of the segment Gly138 - Val150 to Gly114 C(α) from another segment from opposite side of the substrate binding channel in Mycobacterium smegmatis (7.8 Ǻ), Mycobacterium tuberculosis (9.5 Ǻ) and Escherichia coli (11.8 Ǻ). 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(δ2) to Gly113 C(α) in Mycobacterium smegmatis is 4.5 Ǻ while the corresponding distances in Mycobacterium tuberculosis and Escherichia coli are 3.1 Ǻ and 6.7 Ǻ respectively. The hydrogen bonded interactions between Asn116, His22 and Asp95 indicate a stereochemically favorable arrangement of these residues for catalytic action.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-tRNA hydrolase191Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 3.1.1.29
UniProt
Find proteins for A0R3D3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R3D3 
Go to UniProtKB:  A0R3D3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R3D3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.01α = 90
b = 58.98β = 90
c = 62.02γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-08-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-08-05
    Changes: Database references
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Refinement description