PDBsum entry 1okb

Hydrolase

PDB id: 1okb

Contents

Protein chains

223 a.a. *

Ligands

GOL ×2

Metals

_CL ×2

Waters ×343

* Residue conservation analysis

PDB id:

1okb

Name:

Hydrolase

Title:

Crystal structure of uracil-DNA glycosylase from atlantic cod (gadus morhua)

Structure:

Uracil-DNA glycosylase. Chain: a, b. Fragment: catalytic domain, residues 79-301. Engineered: yes. Mutation: yes

Source:

Gadus morhua. Atlantic cod. Organism_taxid: 8049. Organ: liver. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.90Å R-factor: 0.186 R-free: 0.206

Authors:

I.Leiros,E.Moe,O.Lanes,A.O.Smalas,N.P.Willassen

Key ref:

I.Leiros et al. (2003). The structure of uracil-DNA glycosylase from Atlantic cod (Gadus morhua) reveals cold-adaptation features. Acta Crystallogr D Biol Crystallogr, 59, 1357-1365. PubMed id: 12876336 DOI: 10.1107/S0907444903011144

Date:

21-Jul-03 Release date: 05-Apr-04

Protein chains

Q9I983  (Q9I983_GADMO) -  Uracil-DNA glycosylase from Gadus morhua

Seq: 301 a.a.

Struc: 223 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.3.2.2.27 - uracil-DNA glycosylase.

DOI no: 10.1107/S0907444903011144

Acta Crystallogr D Biol Crystallogr 59:1357-1365 (2003)

PubMed id: 12876336

The structure of uracil-DNA glycosylase from Atlantic cod (Gadus morhua) reveals cold-adaptation features.

I.Leiros, E.Moe, O.Lanes, A.O.Smalås, N.P.Willassen.

ABSTRACT

Uracil-DNA glycosylase (UDG; EC 3.2.2.3) is a DNA-repair protein that catalyses the hydrolysis of promutagenic uracil residues from single- or double-stranded DNA, generating free uracil and abasic DNA. The crystal structure of the catalytic domain of cod uracil-DNA glycosylase (cUDG) has been determined to 1.9 A resolution, with final R factors of 18.61 and 20.57% for the working and test sets of reflections, respectively. This is the first crystal structure of a uracil-DNA glycosylase from a cold-adapted species and a detailed comparison with the human enzyme is performed in order to rationalize the cold-adapted behaviour of the cod enzyme at the structural level. The catalytic domain of cUDG comprises 223 residues, with a sequence identity to the human UDG of 75%. The tertiary structures of the two enzymes are also similar, with an overall displacement in main-chain atomic positions of 0.63 A. The amino-acid substitutions and the differences in intramolecular hydrogen bonds, hydrophobic interactions, ion-pair interactions and electrostatic potentials are compared and discussed in order to gain insight into the factors that cause the increased activity and reduced thermostability of the cod enzyme. In particular, the reduced number of strong ion-pair interactions in the C-terminal half of cUDG is believed to greatly affect the flexibility and/or stability. Increased positive electrostatic surface potential on the DNA-facing side of cUDG seems to be responsible for increasing the affinity for the negatively charged DNA compared with that of hUDG.

Selected figure(s)

Figure 1.
Figure 1 Superpositioning of the crystal structures of cUDG (blue) and hUDG (red; PDB code [105]1akz ; Mol et al., 1995[106] [Mol, C. D., Arvai, A. S., Slupphaug, G., Kavli, B., Alseth, I., Krokan, H. E. & Tainer, J. A. (1995). Cell, 80, 869-878.]-[107][bluearr.gif] ). The glycerol molecule bound in the active site of cUDG is included for clarity.

Figure 4.
Figure 4 Estimated electrostatic surface potentials of (a) the crystal structure of cUDG with DNA modelled in and (b) the crystal structure of hUDG-DNA (PDB code [145]1emh ; Parikh et al., 2000[146] [Parikh, S. S., Walcher, G., Jones, G. D., Slupphaug, G., Krokan, H. E., Blackburn, G. M. & Tainer, J. A. (2000). Proc. Natl Acad. Sci. USA, 97, 5083-5088.]-[147][bluearr.gif] ).

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2003, 59, 1357-1365) copyright 2003.

Figures were selected by an automated process.