PDBsum entry 2qy2

Hydrolase, viral protein

PDB id: 2qy2

Contents

Protein chains

224 a.a.

Ligands

ACT ×2

FLC

Waters ×345

PDB id:

2qy2

Name:

Hydrolase, viral protein

Title:

Characterization of a trifunctional mimivirus mRNA capping enzyme and crystal structure of the RNA triphosphatase domainm.

Structure:

Probable mRNA-capping enzyme. Chain: a, b. Engineered: yes

Source:

Mimivirus. Organism_taxid: 315393. Gene: refseq yp_142736. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.00Å R-factor: 0.212 R-free: 0.252

Authors:

S.Shuman,D.Benarroch,P.Smith

Key ref:

D.Benarroch et al. (2008). Characterization of a trifunctional mimivirus mRNA capping enzyme and crystal structure of the RNA triphosphatase domain. Structure, 16, 501-512. PubMed id: 18400173 DOI: 10.1016/j.str.2008.01.009

Date:

13-Aug-07 Release date: 01-Apr-08

Protein chains

Q5UQX1  (MCE_MIMIV) -  Probable mRNA-capping enzyme from Acanthamoeba polyphaga mimivirus

Seq: 1170 a.a.

Struc: 224 a.a.

Enzyme reactions

• Enzyme class 2: E.C.2.1.1.56 - mRNA (guanine-N(7))-methyltransferase.
• Reaction: a 5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L- methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-homocysteine
• Enzyme class 3: E.C.2.7.7.50 - mRNA guanylyltransferase.
• Reaction: a 5'-end diphospho-ribonucleoside in mRNA + GTP + H⁺ = a 5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA + diphosphate
• Enzyme class 4: E.C.3.6.1.74 - mRNA 5'-phosphatase.
• Reaction: a 5'-end triphospho-ribonucleoside in mRNA + H2O = a 5'-end diphospho- ribonucleoside in mRNA + phosphate + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1016/j.str.2008.01.009

Structure 16:501-512 (2008)

PubMed id: 18400173

Characterization of a trifunctional mimivirus mRNA capping enzyme and crystal structure of the RNA triphosphatase domain.

D.Benarroch, P.Smith, S.Shuman.

ABSTRACT

The RNA triphosphatase (RTPase) components of the mRNA capping apparatus are a bellwether of eukaryal taxonomy. Fungal and protozoal RTPases belong to the triphosphate tunnel metalloenzyme (TTM) family, exemplified by yeast Cet1. Several large DNA viruses encode metal-dependent RTPases unrelated to the cysteinyl-phosphatase RTPases of their metazoan host organisms. The origins of DNA virus RTPases are unclear because they are structurally uncharacterized. Mimivirus, a giant virus of amoeba, resembles poxviruses in having a trifunctional capping enzyme composed of a metal-dependent RTPase module fused to guanylyltransferase (GTase) and guanine-N7 methyltransferase domains. The crystal structure of mimivirus RTPase reveals a minimized tunnel fold and an active site strikingly similar to that of Cet1. Unlike homodimeric fungal RTPases, mimivirus RTPase is a monomer. The mimivirus TTM-type RTPase-GTase fusion resembles the capping enzymes of amoebae, providing evidence that the ancestral large DNA virus acquired its capping enzyme from a unicellular host.

Selected figure(s)

Figure 5.
Figure 5. Tertiary Structure of Mimivirus RTPase
(A–F) The fold of mimivirus RTPase (amino acids 11–237) is depicted as a ribbon diagram in (A), (C), and (D); α helices are colored cyan, and β strands are colored magenta. A view into the triphosphate tunnel is highlighted in (A). The N and C termini are indicated. The images in (C) and (D) are rotated clockwise and counterclockwise, respectively, with respect to (A) in order to highlight side views of the staves of the β barrel. (B) shows a space-filling surface model in the same orientation as (A) that highlights the tunnel aperture and an acetate molecule (depicted as a stick model) in the center of the tunnel. The primary structure is displayed in (E); secondary structure elements are highlighted in cyan for α helices and magenta for β strands. The putative metal-binding motifs are located in strands β1 and β8; the essential glutamates are denoted by dots (•). The ^121DIEIVYKN^128 and ^133KLIGI^137 β segments that are interrupted by a short non-β ^129RGSG^132 peptide (indicated by an asterisk in [A]) together comprise one of the barrel staves, which will be considered as a single β element (indicated by brackets in [E]) that corresponds to the fourth β strand of the triphosphate tunnel of yeast Cet1. (F) shows a comparison of the topologies of mimivirus RTPase and yeast Cet1. Tunnel β strands are shown as magenta pentagons oriented in the flat plane according to the view in (A), such that pentagons with the apices pointing into the tunnel in (F) correspond to strands that project out from the page toward the viewer in (A), while pentagons with apices pointing away from the tunnel in (F) are ones that project into the plane of the page in (A). The mimivirus RTPase α helices are shown as cyan circles, as are the corresponding α helices in Cet1. Additional secondary structure elements unique to Cet1 are colored gray. A disordered chain break on the tunnel roof of mimivirus RTPase (from amino acid 155 to amino acid 157 in the loop connecting strands 5 and 6) is indicated by a dashed line. This segment is ordered in the A protomer of the monoclinic crystal, as a result of crystal packing contacts unique to the monoclinic lattice. Chains breaks occurring at different sites in Cet1 are denoted by dashed lines.

Figure 6.
Figure 6. MimiCE RTPase Active Site and Comparison to Cet1
(A and B) Stereo views of the tunnel interiors of (A) MimiCE-(1–237) and (B) yeast Cet1. Waters are depicted as red spheres. The Cet1-bound manganese ion is a cyan sphere. Acetate and sulfate ions in the tunnels are rendered as stick models, as are side chains emanating from the β strands that comprise the tunnel walls.

The above figures are reprinted by permission from Cell Press: Structure (2008, 16, 501-512) copyright 2008.

Figures were selected by an automated process.