crystal structure of porcine RNase 4 D80A mutant in complex with dCMP

Experimental Data Snapshot

  • Resolution: 2.61 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.255 

Starting Model: experimental
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Structural Basis of Substrate Specificity in Porcine Rnase 4.

Liang, S.Acharya, K.R.

(2016) FEBS J 283: 912

  • DOI: https://doi.org/10.1111/febs.13646
  • Primary Citation of Related Structures:  
    5AR6, 5ARJ, 5ARK, 5ARL

  • PubMed Abstract: 

    RNase 4, a member of the RNase A superfamily with substrate preference for uridine, has roles in host defence, angiogenesis and neurodegenerative diseases. It also exhibits the highest interspecies amino acid sequence similarity amongst RNase A family members. However, compared to other members of the RNase A family, including eosinophil-derived neurotoxin, eosinophil cationic protein and angiogenin, little is known about the molecular basis of substrate specificity in RNase 4. Here we report high to medium resolution structures of native porcine RNase 4 (PL3), a 'substrate-specificity' determining mutant D80A and their respective complexes with deoxyuridine 5'-monophosphate (dUMP) and deoxycytidine 5'-monophosphate (dCMP). These structures provide insight into the structural basis of the uridine versus cytosine substrate specificity in RNase 4: in the D80A mutant (D80A•dCMP), the side chain of Arg101 is positioned further away from the substrate-binding pocket due to the loss of the Asp80 side chain, reducing the repulsion force on the less favoured dCMP from Arg101 and allowing the ligand to occupy the binding pocket. This can also explain the observation that the ligand in the D80A•dCMP complex is stabilized only by a small number of hydrogen bonds. Compared to the previously reported structure of the human RNase 4•2'-deoxyuridine 3'-phosphate complex, the structure of PL3•dUMP complex shows additional hydrogen bonds between the ligand and the protein. In addition, the interaction between Arg101 and the dUMP ligand is absent. These observed differences are probably the result of the flexibility and different 'positioning' of the phosphate group among the mononucleotide ligands. The atomic coordinates and structure factors for PL3 (5AR6), D80A (5ARJ), PL3∙dUMP (5ARK) and D80A∙dCMP (5ARL) complexes have been deposited with the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ, USA (http://www.rcsb.org/).

  • Organizational Affiliation

    Department of Biology and Biochemistry, University of Bath, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
134Sus scrofaMutation(s): 1 
EC: 3.1.27
Find proteins for P15468 (Sus scrofa)
Explore P15468 
Go to UniProtKB:  P15468
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15468
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.61 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.255 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.962α = 89.78
b = 62.515β = 79.21
c = 70.216γ = 78.9
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-20
    Type: Initial release
  • Version 1.1: 2016-03-23
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description