PDBsum entry 1euw

Hydrolase

PDB id: 1euw

Contents

Protein chain

136 a.a. *

Ligands

EMC

GOL ×2

Waters ×286

* Residue conservation analysis

PDB id:

1euw

Name:

Hydrolase

Title:

Atomic resolution structure of e. Coli dutpase

Structure:

Deoxyuridine 5'-triphosphate nucleotidohydrolase. Chain: a. Synonym: dutpase. Ec: 3.6.1.23

Source:

Escherichia coli. Organism_taxid: 562

Biol. unit:

Trimer (from PDB file)

Resolution:

1.05Å R-factor: 0.141 R-free: 0.164

Authors:

A.Gonzalez,E.Cedergren,G.Larsson,R.Persson

Key ref:

A.González et al. (2001). Atomic resolution structure of Escherichia coli dUTPase determined ab initio. Acta Crystallogr D Biol Crystallogr, 57, 767-774. PubMed id: 11375495 DOI: 10.1107/S0907444901004255

Date:

17-Apr-00 Release date: 03-May-00

Protein chain

P06968  (DUT_ECOLI) -  Deoxyuridine 5'-triphosphate nucleotidohydrolase from Escherichia coli (strain K12)

Seq: 152 a.a.

Struc: 136 a.a.

Enzyme reactions

• Enzyme class: E.C.3.6.1.23 - dUTP diphosphatase.
• Reaction: dUTP + H2O = dUMP + diphosphate + H⁺

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

reference

DOI no: 10.1107/S0907444901004255

Acta Crystallogr D Biol Crystallogr 57:767-774 (2001)

PubMed id: 11375495

Atomic resolution structure of Escherichia coli dUTPase determined ab initio.

A.González, G.Larsson, R.Persson, E.Cedergren-Zeppezauer.

ABSTRACT

Cryocooled crystals of a mercury complex of Escherichia coli dUTPase diffract to atomic resolution. Data to 1.05 A resolution were collected from a derivative crystal and the structure model was derived from a Fourier map with phases calculated from the coordinates of the Hg atom (one site per subunit of the trimeric enzyme) using the program ARP/wARP. After refinement with anisotropic temperature factors a highly accurate model of the bacterial dUTPase was obtained. Data to 1.45 A from a native crystal were also collected and the 100 K structures were compared. Inspection of the refined models reveals that a large part of the dUTPase remains rather mobile upon freezing, with 14% of the main chain being totally disordered and with numerous side chains containing disordered atoms in multiple discrete conformations. A large number of those residues surround the active-site cavity. Two glycerol molecules (the cryosolvent) occupy the deoxyribose-binding site. Comparison between the native enzyme and the mercury complex shows that the active site is not adversely affected by the binding of mercury. An unexpected effect seems to be a stabilization of the crystal lattice by means of long-range interactions, making derivatization a potentially useful tool for further studies of inhibitor-substrate-analogue complexes of this protein at very high resolution.

Selected figure(s)

Figure 4.
Figure 4 Detail of the 1.05 Å structure, showing parts of the polypeptide chain at the active site, including Tyr93 and one molecule of glycerol (Glyc139). The 2mF[o] - DF[c] electron-density map is contoured at 2 (in blue) and 4 (coral).

Figure 5.
Figure 5 View of the mercury-binding site in a 2mF[o] - DF[c] electron-density map contoured at 3 and 10 (in blue and orange, respectively) showing clearly the multiple conformations of the Hg atom (red spheres) bound to the S of Cys36.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2001, 57, 767-774) copyright 2001.

Figures were selected by an automated process.