The RAGNYA fold: a novel fold with multiple topological variants found in functionally diverse nucleic acid, nucleotide and peptide-binding proteins

Abstract

Using sensitive structure similarity searches, we identify a shared alpha+beta fold, RAGNYA, principally involved in nucleic acid, nucleotide or peptide interactions in a diverse group of proteins. These include the Ribosomal proteins L3 and L1, ATP-grasp modules, the GYF domain, DNA-recombination proteins of the NinB family from caudate bacteriophages, the C-terminal DNA-interacting domain of the Y-family DNA polymerases, the uncharacterized enzyme AMMECR1, the siRNA silencing repressor of tombusviruses, tRNA Wybutosine biosynthesis enzyme Tyw3p, DNA/RNA ligases and related nucleotidyltransferases and the Enhancer of rudimentary proteins. This fold exhibits three distinct circularly permuted versions and is composed of an internal repeat of a unit with two-strands and a helix. We show that despite considerable structural diversity in the fold, its representatives show a common mode of nucleic acid or nucleotide interaction via the exposed face of the sheet. Using this information and sensitive profile-based sequence searches: (1) we predict the active site, and mode of substrate interaction of the Wybutosine biosynthesis enzyme, Tyw3p, and a potential catalytic role for AMMECR1. (2) We provide insights regarding the mode of nucleic acid interaction of the NinB proteins, and the evolution of the active site of classical ATP-grasp enzymes and DNA/RNA ligases. (3) We also present evidence for a bacterial origin of the GYF domain and propose how this version of the fold might have been utilized in peptide interactions in the context of nucleoprotein complexes.

Figure 1.

Representative structures from various families of the RAGNYA fold are shown in the ‘open face’ view. These families encompass the three distinct circularly permuted versions of the fold, whose topology diagrams are shown beside the corresponding structures. The topology diagrams correspond to a 180° rotation about a vertical axis in the plane of paper with respect to the view of the actual structures. The two identical subunits of NinB are shown in different colors in the topology diagram. The figure were made using Pymol. The PDB IDs of the structures are respectively 1JJ2, 1RPU, 1WH2, 1TLJ, 2NML, 1WR2, 1V9P, 1JIH, 1VAJ, 1DWU, 1WSC and 1PC6 (from top to bottom).

Figure 2.

(A) A network representation of structural relationships revealed by the transitive search procedure. The nodes, represented as different shapes in the network, correspond to protein structures while the edges denote the recovery of a hit in the structure similarity search. L3-I, P19, Tyw3 and ER, respectively denote insert domain in Ribosomal protein L3, siRNA silencing repressor of tombusviruses, tRNA Wybutosine biosynthesis enzyme and enhancer of rudimentary. L1 refers to Ribosomal protein L1. The nodes have been colored according to contained circularly permuted version of RAGNYA fold. (B) The three distinct circularly permutated variants and the split version (NinB) of the RAGNYA fold. The existence of circular permutations between domains with topology like L3-I (shown in the middle) and the topologies seen in domains like the classical ATP-grasp module (shown on the left) and Ribosomal protein L1 (shown on the right) are illustrated using pink and green lines and arrows respectively. Also shown below each of the topology diagram are the underlying repeating units of each version of the fold.

Figure 3.

Topology diagrams illustrating various elaborations to the RAGNYA fold seen in the following domains: (A) Tyw3p, which has a SHS2-like domain, shown within the dotted box, inserted between the last two strands (third and fourth strands) of the RAGNYA fold. (B) Classical ATP-grasp module has a protein-kinase-like domain fused to the C-termini of core RAGNYA fold. They possess two conserved lysines, shown in green, one at the C-termini of first strand and the other at the N-terminal extension to the RAGNYA fold. (C) DNA and RNA ligases, possessing close structural congruence to the classical ATP-grasp, have a protein-kinase-like domain inserted between second and third strands of the RAGNYA fold unlike the classical ATP-grasp module. However, they too possess the two conserved lysines, shown in green, at the C-termini of the second and the extension strands, shown in purple color. (D) Ribosomal protein L1 has a TOPRIM-like domain, shown within the dotted box, inserted between first and second strands of the RAGNYA fold. (E) AMMECR1 has two domains with the RAGNYA fold that are interlocked with each other. The exposed cysteine which is potentially involved in likely catalytic role of the protein is shown in brown. The two domains are rotated with respect to each other by more than 90° about a vertical axis indicated in the figure. The sequence of secondary structures shown below reveals that the two domains are related by circular permutations.

Figure 4.

Binding modes of the RAGNYA fold. The four strands of the RAGNYA fold are colored differently and shown in the ‘open face’ view. The topological connectivities which are distinct between the circularly permuted topologies are not shown. The boxes connected to the strands list the domain families that use the strand to bind various ligands. All known structures of RAGNYA domains suggest that the RAGNYA domains bind ligands mainly from the ‘open face’ with the exception of the GYF domain which binds ligands in a ‘side-on’ mode, perhaps in addition to the face on mode. The representative structures from three distinct permuted versions of the RAGNYA fold along with their duplex nucleic acid ligands and a structure of the classical ATP-grasp module with its nucleotide ligand are shown to illustrate the similarity of the binding modes. The PDBIDs of these structures are respectively 1JJ2, 1JX4, 1MZP and 1GSA.

Figure 5.

Phyletic patterns and prominent architectures of the RAGNYA fold domain families are shown. The domain families belonging to distinct permuted versions of the fold are colored differently. The superkingdom-based coloring scheme for the phyletic distribution is indicated below. The dotted lines from a common point denote a hypothesized common origin between families, while the solid lines indicate the presence of evidence to support a common origin. Dotted ellipses encircle a set of families from which a family of more limited phyletic distribution is likely to have diversified. The ‘?’ indicates that the evolutionary origin of the family is unclear. While shown as originating from a common precursor, it should be noted that individual complete versions of the RAGNYA fold might have been independently re-assembled from precursor two strand-one helix units. The prominent architectures of the GYF domain and NinB families are shown. In these architectures abbreviations used for the domain families are: ZnR – zinc ribbon, SPFH – Band 7/SPFH, TPR – tetratricopeptide repeat, DSBH – double-stranded beta helix (cupin-like), TM – transmembrane region, TonB-C – C-terminal domain of TonB and HNH – HNH endonuclease. Representative GIs corresponding to the architectures are the following: NinB+HNH: 116333759, ZnR+GYF+TPR: 121536395, GYF+DSBH: 77747736, SPFH/Band 7+GYF: 32472385 and GYF+TM+TonB-C: 108761942.