PDBsum entry 1st3

Serine protease

PDB id: 1st3

Contents

Protein chain

269 a.a. *

Metals

_CA ×2

Waters ×157

* Residue conservation analysis

PDB id:

1st3

Name:

Serine protease

Title:

The crystal structure of the bacillus lentus alkaline protease, subtilisin bl, at 1.4 angstroms resolution

Structure:

Subtilisin bl. Chain: a. Engineered: yes

Source:

Bacillus lentus. Organism_taxid: 1467

Resolution:

1.40Å R-factor: 0.190

Authors:

D.W.Goddette

Key ref:

D.W.Goddette et al. (1992). The crystal structure of the Bacillus lentus alkaline protease, subtilisin BL, at 1.4 A resolution. J Mol Biol, 228, 580-595. PubMed id: 1453465 DOI: 10.1016/0022-2836(92)90843-9

Date:

22-Nov-91 Release date: 31-Jan-94

Protein chain

P29599  (SUBB_LEDLE) -  Subtilisin BL from Lederbergia lenta

Seq: 269 a.a.

Struc: 269 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.4.21.62 - subtilisin.
• Reaction: Hydrolysis of proteins with broad specificity for peptide bonds, and a preference for a large uncharged residue in P1. Hydrolyzes peptide amides.

DOI no: 10.1016/0022-2836(92)90843-9

J Mol Biol 228:580-595 (1992)

PubMed id: 1453465

The crystal structure of the Bacillus lentus alkaline protease, subtilisin BL, at 1.4 A resolution.

D.W.Goddette, C.Paech, S.S.Yang, J.R.Mielenz, C.Bystroff, M.E.Wilke, R.J.Fletterick.

ABSTRACT

The crystal structure of subtilisin BL, an alkaline protease from Bacillus lentus with activity at pH 11, has been determined to 1.4 A resolution. The structure was solved by molecular replacement starting with the 2.1 A structure of subtilisin BPN' followed by molecular dynamics refinement using X-PLOR. A final crystallographic R-factor of 19% overall was obtained. The enzyme possesses stability at high pH, which is a result of the high pI of the protein. Almost all of the acidic side-chains are involved in some type of electrostatic interaction (ion pairs, calcium binding, etc.). Furthermore, three of seven tyrosine residues have potential partners for forming salt bridges. All of the potential partners are arginine with a pK around 12. Lysine would not function well in a salt bridge with tyrosine as it deprotonates at around the same pH as tyrosine ionizes. Stability at high pH is acquired in part from the pI of the protein, but also from the formation of salt bridges (which would affect the pI). The overall structure of the enzyme is very similar to other subtilisins and shows that the subtilisin fold is more highly conserved than would be expected from the differences in amino acid sequence. The amino acid side-chains in the hydrophobic core are not conserved, though the inter-residue interactions are. Finally, one third of the serine side-chains in the protein have multiple conformations. This presents an opportunity to correlate computer simulations with observed occupancies in the crystal structure.

Selected figure(s)

Figure 6.
Figure 6. The first deletion in subtilisin This stereo Figure shows how Thr36 of subtilisin BL (filled bonds) pans the region occupied by 2 residues in subtilisin BPN' (open bonds). The threonine residue takes on an extended conformation as opposed to a pseudo-helical conformation for residues 36 and 37 in BPN'.

Figure 7.
Figure 7. The scond eletion in subtilisin BL. In this deletion, the (4, @) an gl es of 3 residues are modified slightly to make up the difference. The 3 residues 55 to 57 in subtilisin BL (filled bonds) are equivalent to 4 residues (56 to 59) in subtilisin BPN' (open bonds). The conformations of equivalent glutamine residues at position 57 (59 in BPN') are almost 180'' opposed.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1992, 228, 580-595) copyright 1992.

Figures were selected by an automated process.