PDBsum entry: 1jrk

Structural genomics, unknown function

PDB id: 1jrk

Contents

Protein chains

148 a.a. *

Ligands

MPD ×6

Waters ×173

* Residue conservation analysis

PDB id:

1jrk

Name:

Structural genomics, unknown function

Title:

Crystal structure of a nudix protein from pyrobaculum aerophilum reveals a dimer with intertwined beta sheets

Structure:

Nudix homolog. Chain: a, b, c, d. Engineered: yes. Mutation: yes

Source:

Pyrobaculum aerophilum. Organism_taxid: 13773. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PQS)

Resolution:

2.40Å R-factor: 0.190 R-free: 0.275

Authors:

S.Wang,C.Mura,M.R.Sawaya,D.Cascio,D.Eisenberg

Key ref:

S.Wang et al. (2002). Structure of a Nudix protein from Pyrobaculum aerophilum reveals a dimer with two intersubunit beta-sheets. Acta Crystallogr D Biol Crystallogr, 58, 571-578. PubMed id: 11914479 DOI: 10.1107/S0907444902001191

Date:

13-Aug-01 Release date: 03-Apr-02

Protein chains

Q8ZTD8  (Q8ZTD8_PYRAE) -  MutT/nudix family protein

Seq: 146 a.a.

Struc: 148 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 

• Biochemical function: hydrolase activity (1 term)

DOI no: 10.1107/S0907444902001191

Acta Crystallogr D Biol Crystallogr 58:571-578 (2002)

PubMed id: 11914479

Structure of a Nudix protein from Pyrobaculum aerophilum reveals a dimer with two intersubunit beta-sheets.

S.Wang, C.Mura, M.R.Sawaya, D.Cascio, D.Eisenberg.

ABSTRACT

Nudix proteins, formerly called MutT homolog proteins, are a large family of proteins that play an important role in reducing the accumulation of potentially toxic compounds inside the cell. They hydrolyze a wide variety of substrates that are mainly composed of a nucleoside diphosphate linked to some other moiety X and thus are called Nudix hydrolases. Here, the crystal structure of a Nudix hydrolase from the hyperthermophilic archaeon Pyrobaculum aerophilum is reported. The structure was determined by the single-wavelength anomalous scattering method with data collected at the peak anomalous wavelength of an iridium-derivatized crystal. It reveals an extensive dimer interface, with each subunit contributing two strands to the beta-sheet of the other subunit. Individual subunits consist of a mixed highly twisted and curved beta-sheet of 11 beta-strands and two alpha-helices, forming an alpha-beta-alpha sandwich. The conserved Nudix box signature motif, which contains the essential catalytic residues, is located at the first alpha-helix and the beta-strand and loop preceding it. The unusually short connections between secondary-structural elements, together with the dimer form of the structure, are likely to contribute to the thermostability of the P. aerophilum Nudix protein.

Selected figure(s)

Figure 2.
Figure 2 Ribbon diagrams of the PA Nudix structure. (a) shows the dimer with the twofold NCS axis perpendicular to the paper plane. Each subunit is composed of a long highly twisted central -sheet and a small subsheet connected through strand 2, sandwiched between two -helices. Each subunit contributes two -strands ( 5a and 5b) to the -sheet of the other subunit to form the dimer interface. Subunit A (on the left) has a long C-terminal helix 2 with the eight amino-acid linker at the C-terminal end extending the helix, while subunit B has a shorter helix 2 and its C-terminus and the linker fold back to form a more compact structure. (b) is a near 180° rotation of (a) along a horizontal axis. A cleft formed by the -strands connects helix 1 at the front to the N-terminal end of helix 2 at the back. The conserved arginine and glutamate side chains, as well as two sulfate ions found at the N-terminal end of 2 of each subunit, are shown as sticks. This figure was generated using RIBBONS (Carson, 1997[Carson, M. (1997). Methods Enzymol. 277, 493-505.]).

Figure 5.
Figure 5 Conserved Nudix box residues. The structure around the active site is shown in ribbon representation, with residues in strand 4 and conserved side chains of the catalytic helix shown as sticks. The semi-conserved hydrophobic side chains, Phe46 and Ile52, are also shown. All the conserved side chains are on one side of helix 1, while the side chains of Phe46 and Ile52 are buried and face the central -sheet. Hydrogen bonds from the conserved side chains are shown as red dashed lines.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2002, 58, 571-578) copyright 2002.

Figures were selected by the author.