 |
PDBsum entry 1ibq
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
References listed in PDB file
|
|
|
Key reference
|
|
|
Title
|
|
Structure of aspergillopepsin i from aspergillus phoenicis: variations of the s1'-S2 subsite in aspartic proteinases.
|
|
|
Authors
|
|
S.W.Cho,
N.Kim,
M.U.Choi,
W.Shin.
|
|
|
Ref.
|
|
Acta Crystallogr D Biol Crystallogr, 2001,
57,
948-956.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
