Molecular dynamics refinement of a thermitase-eglin-c complex at 1.98 Å resolution and comparison of two crystal forms that differ in calcium content

Gros, Piet; Betzel, C.; Dauter, Zbigniew; Wilson, K.S.; Hól, Wim G. J.

doi:10.1016/0022-2836(89)90336-7

Cited by 99 publications

(66 citation statements)

References 43 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The coordinates of the crystal structures of subtilisin BPN' in complex with the inhibitor Arg45-eglin (Heinz et al, 1991), and thermitase in complex with eglin (Gros et al, 1989; Brookhaven Protein Data Bank code 1TEC), were used; these structures were chosen because thermitase and subtilisin have the highest sequence identity with NisP, and the Arg45-eglin is suitable for modelling the substrate precursor nisin which also has an Arg(Pl) residue (see below). Four calcium binding sites are known in the subtilase family: a strong (Cal), a medium-strength (Ca2) and two weaker binding sites (Ca3, Ca4;Betzel et al, 1988a;Gros et al, 1989;Tepylakov et al, 1990;Siezen et al, 1991).…”

Section: Coordinatesmentioning

confidence: 99%

“…Four calcium binding sites are known in the subtilase family: a strong (Cal), a medium-strength (Ca2) and two weaker binding sites (Ca3, Ca4;Betzel et al, 1988a;Gros et al, 1989;Tepylakov et al, 1990;Siezen et al, 1991). The Cal and Ca2 ions are present in the thermitase structure used, whereas subtilisin BPN' has the Cal and Ca3 ions and proteinase K has the Ca3 and Ca4 ions.…”

Section: Coordinatesmentioning

confidence: 99%

“…However, the Ca2-embracing loop in NisP is five residues longer than in thermitase (Figure 4), and an additional ligand may be provided by the negatively charged side chain of D I04 in the insert. As in thermitase, the cluster of acidic residues around Ca2 is stabilized further by a conserved, buried Arg residue (Gros et al, 1989), i.e. RI38 in NisP.…”

Section: Calcium Coordination Sitesmentioning

confidence: 99%

“…Residues in subtilases that are in contact with substrate or inhibitor have been identified from crystal structures and modelling of enzyme-inhibitor complexes (Hirono et al, 1984;McPhalen et al, 1985;Bode et al, 1987;Betzel et al, 1988bBetzel et al, , 1993McPhalen and James, 1988;Gros et al, 1989;Dauter et al, 1991;Heinz et al, 1991;Takeuchi et al, 1991a,b) and enzyme-substrate complexes (Wells et al, 1987a), and from protein engineering studies of subtilisin BPN' (Estell et al, 1986;Wells et al, 1987a,b). In each case the mode of substrate-inhibitor binding appears to be essentially the same, and this provides a sound basis for predicting enzyme-substrate interactions in other members of this family.…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Homology modelling of the Lactococcus lactis leader peptidase NisP and its interaction with the precursor of the lantibiotic nisin

Siezen¹,

Rollema²,

Kuipers³

et al. 1995

Protein Eng Des Sel

View full text Add to dashboard Cite

Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim.Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum. Download date: 12-05-2018Protein Engineering vol.8 no.2 pp. [117][118][119][120][121][122][123][124][125] 1995 Homology modelling of the Lactococcus lactis leader peptidase NisP and its interaction with the precursor of the lantibiotic nisin ITo whom correspondence should be addressed A model is presented for the 3-D structure of the catalytic domain of the putative leader peptidase NisP of Lactococcus lactis, and the interaction with its specific substrate, the precursor of the lantibiotic nisin. This homology model is based on the crystal structures of subtilisin BPN' and thermitase in complex with the inhibitor eglin. Predictions are made of the general protein fold, inserted loops, Ca2+ binding sites, aromatic interactions and electrostatic interactions of NisP. Cleavage of the leader peptide from precursor nisin by NisP is the last step in maturation of nisin. A detailed prediction of the substrate binding site attempts to explain the basis of specificity of NisP for precursor nisin. Specific acidic residues in the SI sub site of the substrate binding region of NisP appear to be of particular importance for electrostatic interaction with the PI Arg residue of precursor nisin after which cleavage occurs. The hydrophobic S4 subsite of NisP may also contribute to substrate binding as it does in subtilisins. Predictions of enzyme-substrate interaction were tested by protein engineering of precursor nisin and determining susceptibility of mutant precursors to cleavage by NisP. An unusual property of NisP predicted from this catalytic domain model is a surface patch near the substrate binding region which is extremely rich in aromatic residues. It may be involved in binding to the cell membrane or to hydrophobic membrane proteins, or it may serve as the recognition and binding region for the modified, hydrophobic C-terminal segment of precursor nisin. Similar predictions for the tertiary structure and substrate binding are made for the highly homologous protein EpiP, the putative leader peptidase for the lantibiotic epidermin from Staphylococcus epidermidis, but EpiP lacks the aromatic patch. Based on these models, protein engineering can be employed not only to test the predicted enzyme-substrate interactions, but also to design lantibiotic leader peptidases with a desired specificity.

show abstract

Section: Coordinatesmentioning

confidence: 99%

Section: Coordinatesmentioning

confidence: 99%

Section: Calcium Coordination Sitesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Homology modelling of the Lactococcus lactis leader peptidase NisP and its interaction with the precursor of the lantibiotic nisin

Siezen¹,

Rollema²,

Kuipers³

et al. 1995

Protein Eng Des Sel

View full text Add to dashboard Cite

show abstract

“…The first two enzymes belong to the subgroup containing a single free cysteinyl residue. The three-dimensional crystal structures of proteinase K (Betzel, Pal & Saenger, 1988), of native thermitase (Teplyakov, Kuranova, Harutyunyan, Vainshtein, Fr6mmel, H6hne & Wilson, 1990) and of thermitase complexed with eglin-C (Dauter, Betzel, H6hne, Ingelman & Wilson, 1988;Gros, Betzel, Dauter, Wilson & Hol, 1989;Gros, Fujinaga, Dijkstra, Kalk & Hol, 1989) have been refined at high resolution. Although the overall tertiary fold is similar, and the active-site geometry very similar, these enzymes are substantially less homologous to the Bacilli subtilisins than are the latter among themselves.…”

Section: Bacteriummentioning

confidence: 99%

Complex between the subtilisin from a mesophilic bacterium and the Leech inhibitor eglin-C

Dauter

Betzel²,

Genov³

et al. 1991

Acta Crystallogr Sect B

Self Cite

View full text Add to dashboard Cite

Discovering protein secondary structures: Classification and description of isolated α-turns

Pavone¹,

Gaeta²,

Lombardi³

et al. 1996

Biopolymers

118

View full text Add to dashboard Cite

Molecular dynamics refinement of a thermitase-eglin-c complex at 1.98 Å resolution and comparison of two crystal forms that differ in calcium content

Cited by 99 publications

References 43 publications

Homology modelling of the Lactococcus lactis leader peptidase NisP and its interaction with the precursor of the lantibiotic nisin

Homology modelling of the Lactococcus lactis leader peptidase NisP and its interaction with the precursor of the lantibiotic nisin

Complex between the subtilisin from a mesophilic bacterium and the Leech inhibitor eglin-C

Discovering protein secondary structures: Classification and description of isolated α-turns

Contact Info

Product

Resources

About