PDBsum entry 2b51

Transferase/RNA binding protein

PDB id: 2b51

Contents

Protein chain

444 a.a. *

Ligands

UTP ×3

Metals

_MN

Waters ×325

* Residue conservation analysis

PDB id:

2b51

Name:

Transferase/RNA binding protein

Title:

Structural basis for utp specificity of RNA editing tutases from trypanosoma brucei

Structure:

RNA editing complex protein mp57. Chain: a. Engineered: yes. Mutation: yes

Source:

Trypanosoma brucei. Organism_taxid: 5691. Gene: tbmp57. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.05Å R-factor: 0.189 R-free: 0.227

Authors:

J.Deng,N.L.Ernst,S.Turley,K.D.Stuart,W.G.Hol

Key ref:

J.Deng et al. (2005). Structural basis for UTP specificity of RNA editing TUTases from Trypanosoma brucei. EMBO J, 24, 4007-4017. PubMed id: 16281058 DOI: 10.1038/sj.emboj.7600861

Date:

27-Sep-05 Release date: 22-Nov-05

Protein chain

Q86MV5  (TUT2_TRYBB) -  Terminal uridylyltransferase 2 from Trypanosoma brucei brucei

Seq: 487 a.a.

Struc: 444 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.7.7.52 - Rna uridylyltransferase.
• Reaction: RNA(n) + UTP = RNA(n)-3'-uridine ribonucleotide + diphosphate

RNA(n) + UTP (Bound ligand (Het Group name = UTP) corresponds exactly) = RNA(n)-3'-uridine ribonucleotide + diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1038/sj.emboj.7600861

EMBO J 24:4007-4017 (2005)

PubMed id: 16281058

Structural basis for UTP specificity of RNA editing TUTases from Trypanosoma brucei.

J.Deng, N.L.Ernst, S.Turley, K.D.Stuart, W.G.Hol.

ABSTRACT

Trypanosomatids are pathogenic protozoa that undergo a unique form of post-transcriptional RNA editing that inserts or deletes uridine nucleotides in many mitochondrial pre-mRNAs. Editing is catalyzed by a large multiprotein complex, the editosome. A key editosome enzyme, RNA editing terminal uridylyl transferase 2 (TUTase 2; RET2) catalyzes the uridylate addition reaction. Here, we report the 1.8 A crystal structure of the Trypanosoma brucei RET2 apoenzyme and its complexes with uridine nucleotides. This structure reveals that the specificity of the TUTase for UTP is determined by a crucial water molecule that is exquisitely positioned by the conserved carboxylates D421 and E424 to sense a hydrogen atom on the N3 position of the uridine base. The three-domain structure also unveils a unique domain arrangement not seen before in the nucleotidyltansferase superfamily, with a large domain insertion between the catalytic aspartates. This insertion is present in all trypanosomatid TUTases. We also show that TbRET2 is essential for survival of the bloodstream form of the parasite and therefore is a potential target for drug therapy.

Selected figure(s)

Figure 3.
Figure 3 Overall structure of TbRET2. (A) Ribbon presentation of the molecule. The three domains are shown in green (NTD), yellow (MD) and blue (CTD) (as in Figure 1). The UTP-Mg2+ at site A is shown as ball-and-stick in a cleft between the NTD and the CTD. (B-D) Electrostatic potential surface of TbRET2. The positive and negative regions are colored in blue and red, respectively. Nucleotide-binding sites are labeled in yellow. UTP/UMP and Mg2+ are shown as ball-and-stick. Notice the extended blue patch across three domains that suggests an RNA binding region. (B) Front view, UTP-binding site A with a UTP and nucleotide-binding site B with a UMP molecule; (C) side view (90° upward rotation), nucleotide-binding site B with a UMP molecule; (D) back view (180° upward rotation), nucleotide-binding site C with a UMP molecule. Figure generated by PYMOL (DeLano, 2002).

Figure 5.
Figure 5 UTP-specificity and UMP binding. (A) Interactions of the UTP sugar moiety at site A with the 2'-OH and the side chains of N277 and S278. (B) The uridine base is specifically recognized by Wat1 and D421 and E424. The two hydrogen atoms of Wat1 shown as white spheres makes exquisite hydrogen bonds with O 1 of D421 and O epsilon 1 of E424. The latter two residues are conserved among all trypanosomatid TUTases (Figure 1). (C) UMP binding at site B; (D) UMP binding at site C, which is located far from the active site.

The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2005, 24, 4007-4017) copyright 2005.

Figures were selected by an automated process.