PDBsum entry 1ibq

Hydrolase

PDB id: 1ibq

Contents

Protein chains

325 a.a. *

Ligands

MAN ×4

Metals

_ZN ×8

Waters ×286

* Residue conservation analysis

PDB id:

1ibq

Name:

Hydrolase

Title:

Aspergillopepsin from aspergillus phoenicis

Structure:

Aspergillopepsin. Chain: a, b. Ec: 3.4.23.18

Source:

Aspergillus phoenicis. Organism_taxid: 5063

Resolution:

2.14Å R-factor: 0.221 R-free: 0.269

Authors:

S.W.Cho,W.Shin

Key ref:

S.W.Cho et al. (2001). Structure of aspergillopepsin I from Aspergillus phoenicis: variations of the S1'-S2 subsite in aspartic proteinases. Acta Crystallogr D Biol Crystallogr, 57, 948-956. PubMed id: 11418762 DOI: 10.1107/S0907444901005972

Date:

28-Mar-01 Release date: 04-Jul-01

Protein chains

Q12567  (PEPA_ASPPH) -  Aspergillopepsin-1 from Aspergillus phoenicis

Seq: 394 a.a.

Struc: 325 a.a.

Enzyme reactions

• Enzyme class: E.C.3.4.23.18 - aspergillopepsin I.
• Reaction: Hydrolysis of proteins with broad specificity. Generally favors hydrophobic residues in P1 and P1', but also accepts Lys in P1, which leads to activation of trypsinogen. Does not clot milk.

DOI no: 10.1107/S0907444901005972

Acta Crystallogr D Biol Crystallogr 57:948-956 (2001)

PubMed id: 11418762

Structure of aspergillopepsin I from Aspergillus phoenicis: variations of the S1'-S2 subsite in aspartic proteinases.

S.W.Cho, N.Kim, M.U.Choi, W.Shin.

ABSTRACT

The crystal structure of aspergillopepsin I (AP) from Aspergillus phoenicis has been determined at 2.18 A resolution and refined to R and R(free) factors of 21.5 and 26.0%, respectively. AP has the typical two beta-barrel domain structure of aspartic proteinases. The structures of the two independent molecules are partly different, exemplifying the flexible nature of the aspartic proteinase structure. Notably, the 'flap' in one molecule is closer, with a largest separation of 4.0 A, to the active site than in the other molecule. AP is most structurally homologous to penicillopepsin (PP) and then to endothiapepsin (EP), which share sequence identities of 68 and 56%, respectively. However, AP is similar to EP but differs from PP in the combined S1'-S2 subsite that is delineated by a flexible psi-loop in the C-terminal domain. The S1' and S2 subsites are well defined and small in AP, while there is no definite border between S1' and S2 and the open space for the S2 subsite is larger in PP. Comparison of the structures indicates that the two amino-acid residues equivalent to Leu295 and Leu297 of AP are the major determining factors in shaping the S1'-S2 subsite in the fungal aspartic proteinases.

Selected figure(s)

Figure 4.
Figure 4 A stereoview of the superimposed C^ chains of aspartic proteinases with known structure. Molecules A and B of AP, PP and EP are shown as thick lines in blue, red, yellow and green, respectively, and those of the other aspartic proteinases listed in Table 1-are shown as thin lines in grey. 23 strictly conserved residues are shown as large spheres in yellow for ten glycines and in green for other residues. 44 highly conserved residues are shown as small spheres in orange.

Figure 5.
Figure 5 (a) Superimposed -loop structures of AP, PP and EP: AP is in red, the PP-macrocycle complex is in blue and the EP-pepstatin complex is in yellow. The two ligands are drawn in thin lines. The labelled amino acids are those of AP. (b) Superimposed -loop structures of AP, RP, MP, CP and human pepsin: AP in red, RP in blue, MP in green, CP in pink and human pepsin in yellow. The labelled amino acids are those of human pepsin.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2001, 57, 948-956) copyright 2001.

Figures were selected by the author.