7MPU

Brucella melitensis NrnC bound to pGG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural characterization of NrnC identifies unifying features of dinucleotidases.

Lormand, J.D.Kim, S.K.Walters-Marrah, G.A.Brownfield, B.A.Fromme, J.C.Winkler, W.C.Goodson, J.R.Lee, V.T.Sondermann, H.

(2021) Elife 10

  • DOI: 10.7554/eLife.70146
  • Primary Citation of Related Structures:  
    7MPL, 7MPM, 7MPN, 7MPO, 7MPP, 7MPQ, 7MPR, 7MPS, 7MPT, 7MPU, 7MQB, 7MQC, 7MQD, 7MQE, 7MQF, 7MQG, 7MQH, 7MQI

  • PubMed Abstract: 
  • RNA degradation is fundamental for cellular homeostasis. The process is carried out by various classes of endolytic and exolytic enzymes that together degrade an RNA polymer to mono-ribonucleotides. Within the exoribonucleases, nano-RNases play a unique role as they act on the smallest breakdown products and hence catalyze the final steps in the process ...

    RNA degradation is fundamental for cellular homeostasis. The process is carried out by various classes of endolytic and exolytic enzymes that together degrade an RNA polymer to mono-ribonucleotides. Within the exoribonucleases, nano-RNases play a unique role as they act on the smallest breakdown products and hence catalyze the final steps in the process. We recently showed that oligoribonuclease (Orn) acts as a dedicated diribonucleotidase, defining the ultimate step in RNA degradation that is crucial for cellular fitness (Kim et al., 2019). Whether such a specific activity exists in organisms that lack Orn-type exoribonucleases remained unclear. Through quantitative structure-function analyses we show here that NrnC-type RNases share this narrow substrate length preference with Orn. Although NrnC employs similar structural features that distinguish these two classes as dinucleotidases from other exonucleases, the key determinants for dinucleotidase activity are realized through distinct structural scaffolds. The structures together with comparative genomic analyses of the phylogeny of DEDD-type exoribonucleases indicates convergent evolution as the mechanism of how dinucleotidase activity emerged repeatedly in various organisms. The evolutionary pressure to maintain dinucleotidase activity further underlines the important role these analogous proteins play for cell growth.


    Organizational Affiliation

    Deutsches Elektronen-Synchrotron DESY, Centre for Structural Systems Biology (CSSB), Hamburg, Germany.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NanoRNase CA, B206Brucella melitensisMutation(s): 0 
Gene Names: F6Y32_00630
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-phosphorylated GGC [auth D]2synthetic construct
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.922α = 90
b = 170.922β = 90
c = 85.297γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
Aimlessdata scaling
pointlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI142400

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-15
    Type: Initial release
  • Version 1.1: 2021-09-29
    Changes: Database references