PDBsum entry: 1syd

Hydrolase(phosphoric diester)

PDB id: 1syd

Contents

Protein chain

136 a.a. *

Ligands

THP

Metals

_CA

Waters ×83

* Residue conservation analysis

PDB id:

1syd

Name:

Hydrolase(phosphoric diester)

Title:

Engineering alternative beta-turn types in staphylococcal nuclease

Structure:

Staphylococcal nuclease. Chain: a. Engineered: yes

Source:

Staphylococcus aureus. Organism_taxid: 1280

Resolution:

1.70Å R-factor: 0.184

Authors:

T.R.Hynes,A.Hodel,R.O.Fox

Key ref:

T.R.Hynes et al. (1994). Engineering alternative beta-turn types in staphylococcal nuclease. Biochemistry, 33, 5021-5030. PubMed id: 8172877 DOI: 10.1021/bi00183a004

Date:

07-Jan-94 Release date: 31-Jul-94

Protein chain

P00644  (NUC_STAAU) -  Thermonuclease

Seq: 231 a.a.

Struc: 136 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.

 Gene Ontology (GO) functional annotation 

• Biochemical function: nucleic acid binding (3 terms)

DOI no: 10.1021/bi00183a004

Biochemistry 33:5021-5030 (1994)

PubMed id: 8172877

Engineering alternative beta-turn types in staphylococcal nuclease.

T.R.Hynes, A.Hodel, R.O.Fox.

ABSTRACT

We have refined the crystal structures of three point mutants of staphylococcal nuclease designed to favor alternative beta-turn types. Single amino acid substitutions were made in a type VIa beta-turn (residues 115-118; Tyr-Lys-Pro-Asn) containing a cis Lys 116-Pro 117 peptide bond. The mutations result in two new backbone conformations, a type I beta-turn for P117T and a type I' beta-turn for P117G and P117A. The P117G and P117A structures exhibit a dramatic difference in backbone conformation in the region of the mutation compared to the nuclease A structure such that the side chain of Lys 116 is reoriented to point into the nucleotide binding pocket. The distinct conformation observed for the nuclease A, P117G, and P117T beta-turn sequences agrees with correlations between beta-turn type and sequence identified from protein crystal structures. The P117A turn conformation provides an exception to these correlations. The results demonstrate that single residue changes can significantly alter backbone conformation, illustrating the process by which diversity in the structure of the protein surface can evolve on a conserved structural core, and suggest protein engineering applications in which the positioning as well as the identify of side chains can be modified to design new enzyme functions. Nuclease variants at the type VIa beta-turn site also allow the relationship between the amino acid sequence and beta-turn conformation to be examined in the context of an identical protein fold in crystallographic detail.