PDBsum entry 1kab

Hydrolase(phosphoric diester)

PDB id: 1kab

Contents

Protein chain

136 a.a. *

Waters ×60

* Residue conservation analysis

PDB id:

1kab

Name:

Hydrolase(phosphoric diester)

Title:

Stress and strain in staphylococcal nuclease

Structure:

Staphylococcal nuclease. Chain: a. Engineered: yes

Source:

Staphylococcus aureus. Organism_taxid: 1280

Resolution:

1.80Å R-factor: 0.188

Authors:

A.Hodel,R.O.Fox

Key ref:

A.Hodel et al. (1993). Stress and strain in staphylococcal nuclease. Protein Sci, 2, 838-850. PubMed id: 8495201 DOI: 10.1002/pro.5560020513

Date:

18-Dec-92 Release date: 31-Jan-94

Protein chain

P00644  (NUC_STAAU) -  Thermonuclease from Staphylococcus aureus

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.

DOI no: 10.1002/pro.5560020513

Protein Sci 2:838-850 (1993)

PubMed id: 8495201

Stress and strain in staphylococcal nuclease.

A.Hodel, R.A.Kautz, M.D.Jacobs, R.O.Fox.

ABSTRACT

Protein molecules generally adopt a tertiary structure in which all backbone and side chain conformations are arranged in local energy minima; however, in several well-refined protein structures examples of locally strained geometries, such as cis peptide bonds, have been observed. Staphylococcal nuclease A contains a single cis peptide bond between residues Lys 116 and Pro 117 within a type VIa beta-turn. Alternative native folded forms of nuclease A have been detected by NMR spectroscopy and attributed to a mixture of cis and trans isomers at the Lys 116-Pro 117 peptide bond. Analyses of nuclease variants K116G and K116A by NMR spectroscopy and X-ray crystallography are reported herein. The structure of K116A is indistinguishable from that of nuclease A, including a cis 116-117 peptide bond (92% populated in solution). The overall fold of K116G is also indistinguishable from nuclease A except in the region of the substitution (residues 112-117), which contains a predominantly trans Gly 116-Pro 117 peptide bond (80% populated in solution). Both Lys and Ala would be prohibited from adopting the backbone conformation of Gly 116 due to steric clashes between the beta-carbon and the surrounding residues. One explanation for these results is that the position of the ends of the residue 112-117 loop only allow trans conformations where the local backbone interactions associated with the phi and psi torsion angles are strained. When the 116-117 peptide bond is cis, less strained backbone conformations are available. Thus the relaxation of the backbone strain intrinsic to the trans conformation compensates for the energetically unfavorable cis X-Pro peptide bond. With the removal of the side chain from residue 116 (K116G), the backbone strain of the trans conformation is reduced to the point that the conformation associated with the cis peptide bond is no longer favorable.

Selected figure(s)

Figure 7.
Fig. 7. A: Stereorepresentation of thebackbone of nuclease A (white), KI 16A (green),and KI 16G (blue).Thethreestruc- turesweresuperimpo5edbyminimizingthedifferencebetweenthecoordinates of thebackboneatoms of all residuesexceptthe disorderedloop of residues 44-51 andthe loop containingthemutation(residues 1 11-1 19). Thesidechains of residues 15-1 18 areincluded in thefigure. B: Stereorepresenlationofthesolvent-exposed loop of residues 112-1 8 fromthenuclease A and K116A structue\. The structuresweresuperimpxedasin . Carbonatomsfromnuclease A re hown ingreenand KI 16A carbonatomsareshown in white. C: Stereorepresentation of thesolvent-exposed ofresidues 112-1 18 fromthe K116A and KI 6G structures.Thestructuresweresuperiposedas in A. Carbonatomsfrom KI 6G areshowningreenand I 16A car- bonatomsareshown in white. All oxygenatomsareshown inredandallnit!-ogenatomsareshown inblue.

Figure 8.
Fig. 8. tereorepresentation of heelectrondensitysurroundingresidues116and117intheK116A (A) ndK116G (B) struc- tures.Shownarethe SA-omit F, - F, mapscalculatedusingthenucleaseAmodel(Hynes & Fox, 1991)withresidues112-118 omitted. Eachmapclearlyshowstheisoerizationstate of he 116-117peptide bond. Adetaileddescription of thiscalculation isgiven n theMaterialsandmethods section. Note hatthisisamapfromtheearliestpoint in the refinement.SA-omitmaps havereducedphasebias,butthey also sufferfromweakeneddensityinthearea of omission (Hodel et al., 1992).Furtherre- finement of themodelproducedstrongermaps in whichthe Tyr 115 sidechainappearsinthe position shown. The K116Amap iscontouredat 1.750. The K116G ap is ontouredat 1.50. Carbonatomsarehowninwhite,oxygen atoms are shown in red, andnitrogenatomsareshown in blue.

The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (1993, 2, 838-850) copyright 1993.

Figures were selected by an automated process.