PDBsum entry 1a3v

Nuclease

PDB id: 1a3v

Contents

Protein chain

135 a.a. *

Ligands

THP

Metals

_CA

Waters ×102

* Residue conservation analysis

PDB id:

1a3v

Name:

Nuclease

Title:

Staphylococcal nuclease, cyclopentane thiol disulfide to v23c variant

Structure:

Staphylococcal nuclease. Chain: a. Engineered: yes. Mutation: yes. Other_details: variant formed by chemical modification of sole cysteine residue, pdtp, 3',5'-thymidine diphosphate

Source:

Staphylococcus aureus. Organism_taxid: 1280. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.20Å R-factor: 0.174

Authors:

R.Wynn,P.C.Harkins,F.M.Richards,R.O.Fox

Key ref:

R.Wynn et al. (1997). Comparison of straight chain and cyclic unnatural amino acids embedded in the core of staphylococcal nuclease. Protein Sci, 6, 1621-1626. PubMed id: 9260275 DOI: 10.1002/pro.5560060803

Date:

24-Jan-98 Release date: 29-Apr-98

Protein chain

P00644  (NUC_STAAU) -  Thermonuclease from Staphylococcus aureus

Seq: 231 a.a.

Struc: 135 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

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: 10.1002/pro.5560060803

Protein Sci 6:1621-1626 (1997)

PubMed id: 9260275

Comparison of straight chain and cyclic unnatural amino acids embedded in the core of staphylococcal nuclease.

R.Wynn, P.C.Harkins, F.M.Richards, R.O.Fox.

ABSTRACT

We have determined by X-ray crystallography the structures of several variants of staphylococcal nuclease with long flexible straight chain and equivalent length cyclic unnatural amino acid side chains embedded in the protein core. The terminal atoms in the straight side chains are not well defined by the observed electron density even though they remain buried within the protein interior. We have previously observed this behavior and have suggested that it may arise from the addition of side-chain vibrational and oscillational motions with each bond as a side chain grows away from the relatively rigid protein main chain and/or the population of multiple rotamers (Wynn R, Harkins P, Richards FM. Fox RO. 1996. Mobile unnatural amino acid side chains in the core of staphylococcal nuclease. Protein Sci 5:1026-1031). Reduction of the number of degrees of freedom by cyclization of a side chain would be expected to constrain these motions. These side chains are in fact well defined in the structures described here. Over-packing of the protein core results in a 1.0 A shift of helix 1 away from the site of mutation. Additionally, we have determined the structure of a side chain containing a single hydrogen to fluorine atom replacement on a methyl group. A fluorine atom is intermediate in size between methyl group and a hydrogen atom. The fluorine atom is observed in a single position indicating it does not rotate like methyl hydrogen atoms. This change also causes subtle differences in the packing interactions.

Selected figure(s)

Figure 1.
Fig. 1. Ca of staphylococcal nuclease. Segments are color coded according to secondary structure: Blue, P-sheet; green a-helix.Theside chains of Cys23 and surrounding residues are shown. Close-up of the amino acids that surround residue 23. Residues are labeled next to the a-carbon and color coded according to atom type. The orientation from the left panel is preserved.

Figure 2.
Fig. 2. (F, - F,) position 23 omit maps contoured at 3.5~. Maps were calculated in XF'LOR (Brunger, 1992) and displayed using the program MIDAS (ComputerGraphics Laboratory, University f California, San Francisco).

The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (1997, 6, 1621-1626) copyright 1997.