天冬氨酸蛋白酶内硫醇蛋白酶与偕二醇抑制剂共结晶的初步中子和超高分辨率X射线衍射研究。
Preliminary neutron and ultrahigh-resolution X-ray diffraction studies of the aspartic proteinase endothiapepsin cocrystallized with a gem-diol inhibitor.
作者信息
Tuan Han-Fang, Erskine Peter, Langan Paul, Cooper Jon, Coates Leighton
机构信息
Spallation Neutron Source, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA.
出版信息
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 Dec 1;63(Pt 12):1080-3. doi: 10.1107/S1744309107061283. Epub 2007 Nov 30.
Abstract
Endothiapepsin has been cocrystallized with the gem-diol inhibitor PD-135,040 in a low solvent-content (39%) unit cell, which is unprecedented for this enzyme-inhibitor complex and enables ultrahigh-resolution (1.0 A) X-ray diffraction data to be collected. This atomic resolution X-ray data set will be used to deduce the protonation states of the catalytic aspartate residues. A room-temperature neutron data set has also been collected for joint refinement with a room-temperature X-ray data set in order to locate the H/D atoms at the active site.
摘要
内硫胶蛋白酶已与偕二醇抑制剂PD - 135,040在低溶剂含量（39%）的晶胞中进行了共结晶，这对于这种酶 - 抑制剂复合物来说是前所未有的，并使得能够收集超高分辨率（1.0 Å）的X射线衍射数据。这个原子分辨率的X射线数据集将用于推断催化天冬氨酸残基的质子化状态。还收集了一个室温中子数据集，以便与室温X射线数据集进行联合精修，从而确定活性位点处的H/D原子。
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本文引用的文献
1
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2
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J Mol Biol. 2002 May 17;318(5):1405-15. doi: 10.1016/s0022-2836(02)00197-3.
3
Rearrangement of Cruickshank's formulae for the diffraction-component precision index.
Acta Crystallogr D Biol Crystallogr. 2002 May;58(Pt 5):792-7. doi: 10.1107/s0907444902003931. Epub 2002 Apr 26.
4
Aspartic proteinases in disease: a structural perspective.
Curr Drug Targets. 2002 Apr;3(2):155-73. doi: 10.2174/1389450024605382.
5
A neutron Laue diffraction study of endothiapepsin: implications for the aspartic proteinase mechanism.
Biochemistry. 2001 Nov 6;40(44):13149-57. doi: 10.1021/bi010626h.
6
X-ray-crystallographic studies of complexes of pepstatin A and a statine-containing human renin inhibitor with endothiapepsin.
Biochem J. 1993 Jan 15;289 ( Pt 2)(Pt 2):363-71. doi: 10.1042/bj2890363.
7
Cryoenzymology of penicillopepsin; with an appendix: mechanism of action of aspartyl proteinases.
Biochemistry. 1984 Oct 23;23(22):5247-56. doi: 10.1021/bi00317a024.
8
The active site of aspartic proteinases.
FEBS Lett. 1984 Aug 20;174(1):96-101. doi: 10.1016/0014-5793(84)81085-6.
9
Binding of a reduced peptide inhibitor to the aspartic proteinase from Rhizopus chinensis: implications for a mechanism of action.
Proc Natl Acad Sci U S A. 1987 Oct;84(20):7009-13. doi: 10.1073/pnas.84.20.7009.
10
X-ray analyses of aspartic proteinases. The three-dimensional structure at 2.1 A resolution of endothiapepsin.
J Mol Biol. 1990 Feb 20;211(4):919-41. doi: 10.1016/0022-2836(90)90084-Y.
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