PDBsum entry 1kab

Hydrolase(phosphoric diester)

PDB id

1kab

Contents

			Protein chain

					136 a.a.

			Waters ×60

References listed in PDB file

Key reference

Title

Stress and strain in staphylococcal nuclease.

Authors

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

Ref.

Protein Sci, 1993, 2, 838-850. [DOI no: 10.1002/pro.5560020513]

PubMed id

8495201

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.



	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.

PROCHECK

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