Identification and characterization of an RRM-containing, ELAV-like, RNA binding protein in Acinetobacter Baumannii

Experimental Data Snapshot

  • Resolution: 1.65 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 

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Identification and Characterization of an RRM-Containing, RNA Binding Protein in Acinetobacter baumannii .

Ciani, C.Perez-Rafols, A.Bonomo, I.Micaelli, M.Esposito, A.Zucal, C.Belli, R.D'Agostino, V.G.Bianconi, I.Calderone, V.Cerofolini, L.Massidda, O.Whalen, M.B.Fragai, M.Provenzani, A.

(2022) Biomolecules 12

  • DOI: https://doi.org/10.3390/biom12070922
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Acinetobacter baumannii is a Gram-negative pathogen, known to acquire resistance to antibiotics used in the clinic. The RNA-binding proteome of this bacterium is poorly characterized, in particular for what concerns the proteins containing RNA Recognition Motif (RRM). Here, we browsed the A. baumannii proteome for homologous proteins to the human HuR(ELAVL1), an RNA binding protein containing three RRMs. We identified a unique locus that we called AB - Elavl , coding for a protein with a single RRM with an average of 34% identity to the first HuR RRM. We also widen the research to the genomes of all the bacteria, finding 227 entries in 12 bacterial phyla. Notably we observed a partial evolutionary divergence between the RNP1 and RNP2 conserved regions present in the prokaryotes in comparison to the metazoan consensus sequence. We checked the expression at the transcript and protein level, cloned the gene and expressed the recombinant protein. The X-ray and NMR structural characterization of the recombinant AB-Elavl revealed that the protein maintained the typical β 1 α 1 β 2 β 3 α 2 β 4 and three-dimensional organization of eukaryotic RRMs. The biochemical analyses showed that, although the RNP1 and RNP2 show differences, it can bind to AU-rich regions like the human HuR, but with less specificity and lower affinity. Therefore, we identified an RRM-containing RNA-binding protein actually expressed in A. baumannii .

  • Organizational Affiliation

    Department of Cellular, Computational and Integrative Biology, DeCIBIO, Proteomics and MS Core Facility, University of Trento, 38123 Trento, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hypothetical RNA binding protein from Acinetobacter baumannii98Acinetobacter baumanniiMutation(s): 0 
Gene Names: HMPREF0022_00746
Find proteins for D0CAL6 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
Explore D0CAL6 
Go to UniProtKB:  D0CAL6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0CAL6
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.65 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.56α = 90
b = 69.56β = 90
c = 32.46γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
H2020 Marie Curie Actions of the European CommissionEuropean UnionH2020-MSCA-ITN-2018

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-13
    Type: Initial release
  • Version 1.1: 2022-08-10
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description