PDBsum entry: 1snm

Hydrolase (phosphoric diester)

PDB id: 1snm

Contents

Protein chain

136 a.a. *

Ligands

THP

Metals

_CA

Waters ×60

* Residue conservation analysis

PDB id:

1snm

Name:

Hydrolase (phosphoric diester)

Title:

Active site mutant glu-43 (right arrow) asp in staphylococcal nuclease displays nonlocal structural changes

Structure:

Thermonuclease precursor. Chain: a. Engineered: yes

Source:

Staphylococcus aureus. Organism_taxid: 1280

Resolution:

1.74Å R-factor: 0.174

Authors:

P.J.Loll,E.E.Lattman

Key ref:

P.J.Loll and E.E.Lattman (1990). Active site mutant Glu-43----Asp in staphylococcal nuclease displays nonlocal structural changes. Biochemistry, 29, 6866-6873. PubMed id: 2397218 DOI: 10.1021/bi00481a016

Date:

15-Feb-90 Release date: 15-Jul-91

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/bi00481a016

Biochemistry 29:6866-6873 (1990)

PubMed id: 2397218

Active site mutant Glu-43----Asp in staphylococcal nuclease displays nonlocal structural changes.

P.J.Loll, E.E.Lattman.

ABSTRACT

The crystal structure of the Glu-43----Asp mutant of staphylococcal nuclease complexed with Ca2+ and the inhibitor thymidine 3',5'-bisphosphate (pdTp) has been determined and refined by restrained least-squares methods to a conventional crystallographic R value of 0.174 at a resolution of 1.74 A. Throughout most of the structure, the conformation of the backbone atoms of the mutant is similar to that of the wild-type protein; however, the seemingly conservative mutation Glu----Asp has significantly perturbed the structure of a loop adjacent to the active site, as well as giving rise to looser binding of the essential calcium ion and to a less extensive network of bound water molecules in the active site. Crystal contacts that extend into the active site have also been altered by this amino acid substitution. The changes caused by this mutation are considerably more drastic than would have been predicted and should serve as caveats to those who would draw conclusions about structure-function relationships on the basis of site-directed mutagenesis experiments in the absence of structural data.