PDBsum entry: 1ksl

Lyase

PDB id: 1ksl

Contents

Protein chain

234 a.a. *

Ligands

URA

Waters ×183

* Residue conservation analysis

PDB id:

1ksl

Name:

Lyase

Title:

Structure of rsua

Structure:

Ribosomal small subunit pseudouridine synthase a. Chain: a. Synonym: 16s pseudouridylate 516 synthase, 16s pseudouridine 516 synthase, uracil hydrolyase. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.10Å R-factor: 0.226 R-free: 0.258

Authors:

J.Sivaraman,V.Sauve,R.Larocque,E.A.Stura,J.D.Schrag, M.Cygler,A.Matte,Montreal-Kingston Bacterial Structural Genomics Initiative (Bsgi)

Key ref:

J.Sivaraman et al. (2002). Structure of the 16S rRNA pseudouridine synthase RsuA bound to uracil and UMP. Nat Struct Biol, 9, 353-358. PubMed id: 11953756 DOI: 10.1038/nsb788

Date:

13-Jan-02 Release date: 24-Apr-02

Protein chain

P0AA43  (RSUA_ECOLI) -  Ribosomal small subunit pseudouridine synthase A

Seq: 231 a.a.

Struc: 234 a.a.

Enzyme reactions

• Enzyme class: E.C.5.4.99.19 - 16S rRNA pseudouridine(516) synthase.
• Reaction: 16S rRNA uridine₅₁₆ = 16S rRNA pseudouridine₅₁₆

 Gene Ontology (GO) functional annotation 

• Biological process: RNA modification (3 terms)
• Biochemical function: protein binding (5 terms)

DOI no: 10.1038/nsb788

Nat Struct Biol 9:353-358 (2002)

PubMed id: 11953756

Structure of the 16S rRNA pseudouridine synthase RsuA bound to uracil and UMP.

J.Sivaraman, V.Sauvé, R.Larocque, E.A.Stura, J.D.Schrag, M.Cygler, A.Matte.

ABSTRACT

In Escherichia coli, the pseudouridine synthase RsuA catalyzes formation of pseudouridine (psi) at position 516 in 16S rRNA during assembly of the 30S ribosomal subunit. We have determined the crystal structure of RsuA bound to uracil at 2.0 A resolution and to uridine 5'-monophosphate (UMP) at 2.65 A resolution. RsuA consists of an N-terminal domain connected by an extended linker to the central and C-terminal domains. Uracil and UMP bind in a cleft between the central and C-terminal domains near the catalytic residue Asp 102. The N-terminal domain shows structural similarity to the ribosomal protein S4. Despite only 15% amino acid identity, the other two domains are structurally similar to those of the tRNA-specific psi-synthase TruA, including the position of the catalytic Asp. Our results suggest that all four families of pseudouridine synthases share the same fold of their catalytic domain(s) and uracil-binding site.

Selected figure(s)

Figure 1.
Figure 1. Overall structure of RsuA. a, Ribbon diagram of RsuA. The N-terminal domain (residues 1−55, 1- 1- 2- 2- 6) is red, the central domain (residues 62−128, 7- 3- 8- 9- 4, and 207−231, 14- 15- 7) is blue and cyan, respectively, and the C-terminal domain (residues 129−206, 11- 5- 12- 10- 6- 13) is green. An extended polypeptide linker (residues 56−61) between the N-terminal and central domains is yellow. Regions of the protein sequence that correspond to the conserved sequence motifs I, II and III (orange) cluster near the active site cleft. UMP and Asp 102 are depicted in ball-and-stick representation. -strands and -helices are labeled consecutively throughout the structure. b, Stereo view of the C backbone of RsuA bound to UMP, with every 20^th residue numbered. The combined central and C-terminal domains from RsuA−UMP (thick lines) and RsuA−uracil (thin lines), representing two nonisomorphous crystals, were superimposed in O^32. The flexibility of the N-terminal domain with respect to the catalytic module is shown. This figure was prepared using MolScript^34 and Raster3D^35.

Figure 2.
Figure 2. Uracil- and UMP-binding sites. a, Simulated annealing F[o] − F[c] omit map in stereo showing electron density for uracil bound to RsuA. All atoms within 4 Å were omitted from refinement. Two orientations for uracil consistent with the electron density are modeled, related by a rotation of the ring by 180° about the atoms N1−C4. The map is contoured at 2.5 . b, Simulated annealing F[o] − F[c] omit map showing electron density for UMP bound to RsuA. All atoms within 2 Å were omitted from refinement. This map is contoured at 2 . Thin black lines indicate hydrogen bonds here and in (a). Figures were prepared using BobScript^36. c, The key intermediate of the proposed catalytic mechanism^10, ^24 of pseudouridine synthases that shares similarities with that of the retaining glycoside hydrolases. Nucleophilic attack of the Asp at C1' of ribose forms the depicted covalent intermediate, with concomitant breakage of the N-glycosidic bond. This is followed by rotation of the uracil ring such that C5 of the base is adjacent to C1' and, finally, formation of the new C1'−C5 bond. d, In an alternative mechanism^24, the Asp attacks C6 of uracil, forming the depicted covalent intermediate (Michael adduct), followed by breakage of the glycosidic bond. Rotation of the uracil ring by 180° along the C6−N3 axis of the base brings C5 adjacent to C1' of ribose, ready for formation of the new C−C bond.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2002, 9, 353-358) copyright 2002.

Figures were selected by the author.

Author's comment

Note the flexible linker between the S4-like N-term domain and the catalytic domain. In the structure of the same enzyme from H. influenzae (PDB 1vio), this linker is bent at an almost 90 degree angle, bringing the two domains into contact.
Allan Matte