PDBsum entry 1vlr

RNA binding protein

PDB id: 1vlr

Contents

Protein chains

290 a.a. *

Ligands

EDO ×6

Waters ×812

* Residue conservation analysis

PDB id:

1vlr

Name:

RNA binding protein

Title:

Crystal structure of mRNA decapping enzyme (dcps) from mus musculus at 1.83 a resolution

Structure:

mRNA decapping enzyme. Chain: a, b. Synonym: histidine triad protein member 5. Engineered: yes

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Gene: dcps. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

1.83Å R-factor: 0.161 R-free: 0.201

Authors:

Joint Center For Structural Genomics (Jcsg)

Key ref:

G.W.Han et al. (2005). Crystal structure of an Apo mRNA decapping enzyme (DcpS) from Mouse at 1.83 A resolution. Proteins, 60, 797-802. PubMed id: 16001405 DOI: 10.1002/prot.20467

Date:

10-Aug-04 Release date: 24-Aug-04

Protein chains

Q9DAR7  (DCPS_MOUSE) -  m7GpppX diphosphatase from Mus musculus

Seq: 338 a.a.

Struc: 290 a.a.

Enzyme reactions

• Enzyme class: E.C.3.6.1.59 - 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase.
• Reaction: a 5'-end (N₇-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + H2O = N(7)-methyl-GMP + a 5'-end diphospho-ribonucleoside in mRNA + 2 H⁺

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

reference

DOI no: 10.1002/prot.20467

Proteins 60:797-802 (2005)

PubMed id: 16001405

Crystal structure of an Apo mRNA decapping enzyme (DcpS) from Mouse at 1.83 A resolution.

G.W.Han, R.Schwarzenbacher, D.McMullan, P.Abdubek, E.Ambing, H.Axelrod, T.Biorac, J.M.Canaves, H.J.Chiu, X.Dai, A.M.Deacon, M.DiDonato, M.A.Elsliger, A.Godzik, C.Grittini, S.K.Grzechnik, J.Hale, E.Hampton, J.Haugen, M.Hornsby, L.Jaroszewski, H.E.Klock, E.Koesema, A.Kreusch, P.Kuhn, S.A.Lesley, T.M.McPhillips, M.D.Miller, K.Moy, E.Nigoghossian, J.Paulsen, K.Quijano, R.Reyes, G.Spraggon, R.C.Stevens, H.van den Bedem, J.Velasquez, J.Vincent, A.White, G.Wolf, Q.Xu, K.O.Hodgson, J.Wooley, I.A.Wilson.

ABSTRACT

No abstract given.

Selected figure(s)

Figure 1.
Figure 1. Crystal structure of mRNA decapping enzyme (DcpS) from Mouse. (A) Stereo ribbon diagram of Mouse DcpS color-coded from N-terminus (blue) to C-terminus (red) showing the domain organization with helices H1-H13 and -strands 1- 14, as well as -sheets A, B, C, and D. (B) Diagram showing the secondary structure elements in Mouse DcpS (chain A) superimposed on its primary sequence. The -sheet strands are indicated by a red A, B, C, and D. -bulges and -turns are indicated. -hairpins are depicted as red loops. Disordered regions are depicted by a dashed line with the corresponding sequence in brackets. The HIT sequence motif is indicated by a black line above the three histidines.

Figure 2.
Figure 2. Comparison of Mouse and human DcpS. (A) Ribbon diagram of the Mouse DcpS dimer. Chain A is in gray and chain B is in pink. The dimer is symmetric with a C -C distance between Asp110 and Trp174 of 28 Å. Residues 131 and 147 flanking the linker region are labeled. (B) Ribbon diagram of the human DcpS/mGpppG complex. Chain A is shown in gray and chain B in purple. The dimer has a symmetric bottom and an asymmetric top and features an open side and a closed side with a 36 Å and 6 Å C -C gap between Asp111 and Trp175, respectively. The mGpppG nucleotides bound to the active sites are shown in ball-and-stick configuration, with carbon atoms colored in yellow, phosphorous in purple, oxygen in red, and nitrogen in blue. The movement of the N-terminal domain is facilitated by a conformational change in the linker region around helix 3. Superposition of the DcpS active sites in the relaxed empty state with the open (C) and closed (D) mGpppG bound state. The mGpppG-interacting residues from human DcpS (gray, residues labeled in brackets) and their counterparts in Mouse DcpS (blue) are shown in ball-and-stick configuration.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2005, 60, 797-802) copyright 2005.