Structural basis of porcine RNase 4 recognition

  • Shutian Liang

Student thesis: Doctoral ThesisPhD


Bovine pancreatic ribonuclease (RNase A) and its homologues are pyrimidine-specific ribonucleases widely present in mammals, birds, amphibians, reptiles, and fish. RNases recognise a specific sequence – an adenosine 3' to a pyrimidine – on RNA, and cleave the molecule on the 3' side of the 3'-phosphate of the pyrimidine base. Extensive studies have been carried out on the RNase A homologues, including eosinophil-derived neurotoxin (EDN; RNase 2), eosinophil cationic protein (ECP; RNase 3), and angiogenin (ANG; RNase 5), and revealed distinct biological functions: EDN and ECP are involved in neurotoxicity, and ANG possesses angiogenic activity. RNase 4, although being discovered for a long time, is not as well characterised as much as other RNases.RNase 4 has been found in several mammalian species including a few primates, porcine, bovine, and rodents. The mature protein of RNase 4 consists of 119 amino acids, making it the shortest amongst all RNase A homologues. It has a higher inter-species similarity than its homologues, and such high evolutionary conservation suggests that RNase 4 has a more specialised function than RNA degradation. While RNase A, EDN, ECP, and ANG show cytidine preference, RNase 4 has a strong preference for uridine, which can be reversed back to cytidine by a single amino acid substitution of Asp-80, as shown by studies performed with porcine RNase 4 (also known as PL3).In this study, we used PL3 as a model to study the substrate specificity of RNase 4, and have solved four structures, including PL3, PL3 D80A mutant, and these two proteins in complex with dUMP and dCMP respectively. PL3 adopts the classic kidney-shaped RNase A fold, and residues forming the substrate binding subsites occupy similar positions as those in human RNase 4 and the prototypic RNase A. The structure of PL3 D80A mutant resembles that of the wild typeiiiPL3, and only hydrogen bond interactions between the side chains of Asp-80 and Arg-101 are lost.The structure of PL3·dUMP complex revealed interactions between the dUMP and residues Arg-7, His-12, Thr-44 and Phe-117 of PL3, which were also observed in the structure of human RNase 4 in complex with dUp. The additional hydrogen bonds identified between dUMP and residues Gln-11, Lys-40, Asn-43, and Lys-119 of PL3, as well as the absence of the interactions between Arg-101 of PL3 and the ligand that were present in the hRNase 4·dUp structure, could be due to the flexibility of the mononucleotide ligand.The crystal structure of PL3 D80A·dCMP complex presents a small number of hydrogen bond interactions between the protein and the dCMP ligand, which might be sufficient to stabilise the ligand in the B1 subsite, as the repulsion force on the dCMP ligand from the side chain of Arg-101 is absent in the PL3 D80A mutant. This is because in the D80A mutant, Ala-80 cannot provide hydrogen bonding that would hold the side chain of Arg-101 towards the B1 subsite.The activities of RNases can be inhibited by a 50 kDa cytosolic protein, the natural ribonuclease inhibitor (RI). RI binds to all the members of the RNase A superfamily, thus regulating the cytoplasmic RNA levels and protecting cells from inappropriately secreted RNases. The interactions between RNase and RI are tight, reversible, and in a 1:1 ratio. Several complex structures of RNase·RI from various species have been determined, and the residues in the interfaces between RNase and RI are conserved in all of the complexes. Studies revealed a 17-fold tighter interaction between PL3 and human RI than RNase A, making it very interesting to study the structure of the PL3·RI complex and characterise the interactions between PL3 and RI proteins.ivTo date, we have established purification protocols for both proteins, and the next step towards the structure of PL3·RI would be to prepare and purify the protein complex, subject the protein complex to crystallisation experiments, and eventually lead us to the structural determination of PL3·RI complex.
Date of Award3 May 2015
Original languageEnglish
Awarding Institution
  • University of Bath
SupervisorRavi Acharya (Supervisor)


  • X-ray crystallography

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