PDBsum entry 3d6c

Hydrolase

PDB id: 3d6c

Contents

Protein chain

135 a.a. *

Ligands

THP

Metals

_CA

Waters ×93

* Residue conservation analysis

PDB id:

3d6c

Name:

Hydrolase

Title:

Crystal structure of staphylococcal nuclease variant phs l38e at cryogenic temperature

Structure:

Thermonuclease. Chain: a. Fragment: sequence database residues 83-231. Synonym: tnase, micrococcal nuclease, staphylococcal nuclease, nuclease b, nuclease a. Engineered: yes. Mutation: yes

Source:

Staphylococcus aureus. Organism_taxid: 1280. Gene: nuc. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.00Å R-factor: 0.179 R-free: 0.234

Authors:

M.J.Harms,J.L.Schlessman,G.R.Sue,E.B.Garcia-Moreno

Key ref:

M.J.Harms et al. (2009). The pK(a) values of acidic and basic residues buried at the same internal location in a protein are governed by different factors. J Mol Biol, 389, 34-47. PubMed id: 19324049 DOI: 10.1016/j.jmb.2009.03.039

Date:

19-May-08 Release date: 04-Nov-08

Protein chain

P00644  (NUC_STAAU) -  Thermonuclease from Staphylococcus aureus

Seq: 231 a.a.

Struc: 135 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.1.31.1 - micrococcal nuclease.
• Reaction: Endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotide end-products.

DOI no: 10.1016/j.jmb.2009.03.039

J Mol Biol 389:34-47 (2009)

PubMed id: 19324049

The pK(a) values of acidic and basic residues buried at the same internal location in a protein are governed by different factors.

M.J.Harms, C.A.Castañeda, J.L.Schlessman, G.R.Sue, D.G.Isom, B.R.Cannon, B.García-Moreno E.

ABSTRACT

The pK(a) values of internal ionizable groups are usually very different from the normal pK(a) values of ionizable groups in water. To examine the molecular determinants of pK(a) values of internal groups, we compared the properties of Lys, Asp, and Glu at internal position 38 in staphylococcal nuclease. Lys38 titrates with a normal or elevated pK(a), whereas Asp38 and Glu38 titrate with elevated pK(a) values of 7.0 and 7.2, respectively. In the structure of the L38K variant, the buried amino group of the Lys38 side chain makes an ion pair with Glu122, whereas in the structure of the L38E variant, the buried carboxyl group of Glu38 interacts with two backbone amides and has several nearby carboxyl oxygen atoms. Previously, we showed that the pK(a) of Lys38 is normal owing to structural reorganization and water penetration concomitant with ionization of the Lys side chain. In contrast, the pK(a) values of Asp38 and Glu38 are perturbed significantly owing to an imbalance between favorable polar interactions and unfavorable contributions from dehydration and from Coulomb interactions with surface carboxylic groups. Their ionization is also coupled to subtle structural reorganization. These results illustrate the complex interplay between local polarity, Coulomb interactions, and structural reorganization as determinants of pK(a) values of internal groups in proteins. This study suggests that improvements to computational methods for pK(a) calculations will require explicit treatment of the conformational reorganization that can occur when internal groups ionize.

Selected figure(s)

Figure 1.
Fig. 1. Crystal structure of PHS/L38E (pink, PDB accession code 3D6C) overlaid on the structures of PHS/L38K (blue, PDB accession code 2RKS) and PHS nuclease (white, PDB accession code 1EY8). (a) The global fold of the protein is not perturbed. The C^α atoms of Asp and Glu residues are shown as red spheres. Glu38, Lys38, and Glu122 are shown as sticks. (b) Microenvironment of Glu38 and Lys38. Ionizable residues within 8.4 Å of Glu38 are shown in stick, and hydrogen bonds are shown as broken lines.

Figure 6.
Fig. 6. Distance dependence of apparent Coulomb interactions for the current study (●) and for data published previously by Lee et al. ( Image )^29 and Baran et al. ( Image ).^30 The broken line is a fit to the data from the current study only, whereas the continuous line is a fit to all available data.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2009, 389, 34-47) copyright 2009.

Figures were selected by an automated process.