PDBsum entry: 1sta

Hydrolase(phosphoric diester)

PDB id: 1sta

Contents

Protein chain

137 a.a. *

Ligands

THP

Metals

_CA

Waters ×93

* Residue conservation analysis

PDB id:

1sta

Name:

Hydrolase(phosphoric diester)

Title:

Accommodation of insertion mutations on the surface and in the interior of staphylococcal nuclease

Structure:

Staphylococcal nuclease. Chain: a. Engineered: yes

Source:

Staphylococcus aureus. Organism_taxid: 1280

Resolution:

1.70Å R-factor: 0.182

Authors:

L.J.Keefe,S.Quirk,A.Gittis,E.E.Lattman

Key ref:

L.J.Keefe et al. (1994). Accommodation of insertion mutations on the surface and in the interior of staphylococcal nuclease. Protein Sci, 3, 391-401. PubMed id: 8019410 Ref: Full text

Date:

17-Jan-94 Release date: 22-Jun-94

Protein chain

P00644  (NUC_STAAU) -  Thermonuclease

Seq: 231 a.a.

Struc: 137 a.a.*

* PDB and UniProt seqs differ at 2 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.

 Gene Ontology (GO) functional annotation 

• Biochemical function: nucleic acid binding (3 terms)

Full text	Protein Sci 3:391-401 (1994)
PubMed id: 8019410

Accommodation of insertion mutations on the surface and in the interior of staphylococcal nuclease.

L.J.Keefe, S.Quirk, A.Gittis, J.Sondek, E.E.Lattman.

ABSTRACT

Alignment of homologous amino acid sequences reveals that insertion mutations are fairly common in evolution. Hitherto, the structural consequences of insertion mutations on the surface and in the interior of proteins of known structures have received little attention. We report here the high-resolution X-ray crystal structures of 2 site-directed insertion mutants of staphylococcal nuclease. The structure of the first insertion mutant, in which 2 glycine residues were inserted on the protein surface in the amino-terminal beta-strand, has been solved to 1.70 A resolution and refined to a crystallographic R value of 0.182. The inserted residues are accommodated in a special 3-residue beta-bulge. A bridging water molecule in the newly created cavity satisfies the hydrogen bonding requirements of the beta-sheet by forming a bifurcated hydrogen bond to 1 beta-strand, and a single hydrogen bond to the other beta-strand. The second insertion mutant contains a single leucine residue inserted at the end of the third beta-strand. The structure was solved to 2.0 A resolution and refined to a final R value of 0.196. The insertion is accommodated in a register shift that changes the conformation of the flexible loop portion of the molecule, relaxing and widening the omega turn. This structural alteration results in changes in position and coordination of a bound calcium ion important for catalysis. These structures illustrate important differences in how amino acid insertions are accommodated: as localized bulges, and as extensive register shifts.

Selected figure(s)

Figure 2.
Fig. 2. Variation of R value with resolution for the insertion mutant 11GG12 (A) and 36L3 (B). Theoretical curves indicated are for mean positionalerrors between 0.2 and 0.5 A. For 11GG12, the highest res- olution shell of data (from 1.70 to .79 is only -20% complete.

Figure 4.
Fig. 4. Comparison of the hydrogen bond- Ile 72 ing networks in the NH2-terminal &strands f wild-type staphylococcal nuclease and of he insertion mutant llGG12. The back- oneatoms of the wild-type protein re in A; those of lGG12 are shown in B. Hydrogen bondsare represented by dashed lines. In B, a bridging water mole- cule in the special 3-residue @-bulge hydro- en bonds to the carbonyl groups f Glu IO (2.73 A) and fthe first inserted glycine (Gly la) (2.96 A) andto theamidegroup of Val 74 (2.93 A). This figure was generated using QUANTA (Polygen, 1990). in C is a schematic diagram (Chan et al., 993) of thehydrogenbonding in the special 3-residue &bulge in llGG12. Hydrogen bonds are represented by arrows and the di- rection of side chains in the &sheet are in- dicated by + and - signs. In both Band C, the residues in the bulge are labeled X, 1, 2, and 3.

The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (1994, 3, 391-401) copyright 1994.

Figures were selected by an automated process.