Blundell T L, Jenkins J A, Sewell B T, Pearl L H, Cooper J B, Tickle I J, Veerapandian B, Wood S P
Department of Crystallography, Birkbeck College, University of London, England.
J Mol Biol. 1990 Feb 20;211(4):919-41. doi: 10.1016/0022-2836(90)90084-Y.
The molecular structure of endothiapepsin (EC 3.4.23.6), the aspartic proteinase from Endothia parasitica, has been refined to a crystallographic R-factor of 0.178 at 2.1 A resolution. The positions of 2389 protein non-hydrogen atoms have been determined and the present model contains 333 solvent molecules. The structure is bilobal, consisting of two predominantly beta-sheet domains that are related by an approximate 2-fold axis. Of approximately 170 residues, 65 are topologically equivalent when one lobe is superimposed on the other. Twenty beta-strands are arranged as five beta-sheets and are connected by regions involving 29 turns and four helices. A central sheet involves three antiparallel strands from each lobe organized around the dyad axis. Each lobe contains a further local dyad that passes through two sheets arranged as a sandwich and relates two equivalent motifs of four antiparallel strands (a, b, c, d) followed by a helix or an irregular helical region. Sheets 1N and 1C, each contain two interpenetrating psi structures contributed by strands c,d,d' and c',d',d, which are related by the intralobe dyad. A further sheet, 2N or 2C, is formed from two extended beta-hairpins from strands b,c and b',c' that fold above the sheets 1N and 1C, respectively, and are hydrogen-bonded around the local intralobe dyad. Asp32 and Asp215 are related by the interlobe dyad and form an intricate hydrogen-bonded network with the neighbouring residues and comprise the most symmetrical part of the structure. The side-chains of the active site aspartate residues are held coplanar and the nearby main chain makes a "fireman's grip" hydrogen-bonding network. Residues 74 to 83 from strands a'N and b'N in the N-terminal lobe form a beta-hairpin loop with high thermal parameters. This "flap" projects over the active site cleft and shields the active site from the solvent region. Shells of water molecules are found on the surface of the protein molecule and large solvent channels are observed within the crystal. There are only three regions of intermolecular contacts and the crystal packing is stabilized by many solvent molecules forming a network of hydrogen bonds. The three-dimensional structure of endothiapepsin is found to be similar to two other fungal aspartic proteinases, penicillopepsin and rhizopuspepsin. Even though sequence identities of endothiapepsin with rhizopuspepsin and penicillopepsin are only 41% and 51%, respectively, a superposition of the three-dimensional structures of these three enzymes shows that 237 residues (72%) are within a root-mean-square distance of 1.0 A.
寄生内座壳天冬氨酸蛋白酶（EC 3.4.23.6）的分子结构已精修至2.1 Å分辨率下晶体学R因子为0.178。已确定2389个蛋白质非氢原子的位置，当前模型包含333个溶剂分子。该结构为双叶型，由两个主要为β折叠片层结构域组成，通过一个近似2次对称轴相关联。在大约170个残基中，当一个叶瓣与另一个叶瓣叠合时，65个残基在拓扑结构上是等效的。20条β链排列成5个β折叠片层，并由涉及29个转角和4个螺旋的区域相连。一个中央片层围绕二重轴由每个叶瓣的三条反平行链组成。每个叶瓣还包含一个局部二重轴，其穿过两个堆叠在一起的片层，并关联四个反平行链（a、b、c、d）随后是一个螺旋或不规则螺旋区域的两个等效基序。片层1N和1C各自包含由链c、d、d'和c'、d'、d贡献的两个相互贯穿的ψ结构，它们通过叶瓣内二重轴相关联。另一个片层2N或2C由链b、c和b'、c'的两个延伸β发夹形成，分别在片层1N和1C上方折叠，并围绕局部叶瓣内二重轴形成氢键。Asp32和Asp215通过叶瓣间二重轴相关联，并与相邻残基形成复杂的氢键网络，构成结构中最对称的部分。活性位点天冬氨酸残基的侧链保持共面，附近的主链形成一个“消防员抓握”氢键网络。N端叶瓣中来自链a'N和b'N的74至83位残基形成一个具有高热参数的β发夹环。这个“瓣”突出于活性位点裂隙上方，将活性位点与溶剂区域隔开。在蛋白质分子表面发现有水分子壳层，在晶体内观察到有大的溶剂通道。仅有三个分子间接触区域，晶体堆积通过许多形成氢键网络的溶剂分子得以稳定。发现寄生内座壳天冬氨酸蛋白酶的三维结构与另外两种真菌天冬氨酸蛋白酶，即青霉天冬氨酸蛋白酶和根霉天冬氨酸蛋白酶相似。尽管寄生内座壳天冬氨酸蛋白酶与根霉天冬氨酸蛋白酶和青霉天冬氨酸蛋白酶的序列同一性分别仅为41%和51%，但这三种酶的三维结构叠合显示，237个残基（72%）在均方根距离1.0 Å范围内。
