Structural evidence for stabilization of inhibitor binding by a protein cavity in the dehaloperoxidase-hemoglobin from Amphitrite ornata
Structural evidence for stabilization of inhibitor binding by a protein cavity in the dehaloperoxidase-hemoglobin from Amphitrite ornata
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DOI：
10.1002/bip.21674
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发表时间：
2012-01-01
期刊：
影响因子：
2.9
通讯作者：
Franzen, Stefan
中科院分区：
文献类型：
--
作者：
de Serrano, Vesna;Franzen, Stefan
一个稳定抑制剂结合的蛋白质腔的功能作用已经建立的基础上比较的Xe-衍生化和dichor-bound的X-射线晶体结构中的脱卤过氧化物酶-血红蛋白（DHPA）的装饰的Amphitrite。四种不同的抑制剂，4-氟苯酚，4-氯苯酚，4-溴苯酚，和4-碘苯酚在远端口袋中的内部结合亲和力已被证明以前增加的对位卤素原子的半径成比例。天然底物2，4，6-三溴苯酚的氧化抑制已被证明遵循抑制剂结合强度的趋势，因为双位点竞争性抑制机制涉及底物被抑制剂置换，该抑制剂在涉及DHPA的远端组氨酸的门控机制中。在这项研究中，它示出了一个较大的对位卤素取代基的较强的结合的起源在结构上与X射线晶体学的结构特征的Xe结合腔（Xe 1）相一致。Xe 1位点被远端口袋中的氨基酸残基L100、F21、F24、F35、F60和V59包围，位于距血红素铁4.8埃的位置，与抑制剂4-溴苯酚的对溴原子重合。4-溴苯酚普遍存在于底栖生态系统中，其中A.装饰居住。标记为Xe 2的DHPA中的第二个不太明确的结合位点位于蛋白质表面附近的氨基酸残基L 62、R69、D 79、T82和L 83附近，其可能与DHPA表面上的底物对接有关。(c)2011 Wiley Periodicals，Inc. Biopolymers（Pept Sci）98：2735，2012.
A functional role for a protein cavity that stabilizes inhibitor binding has been established based on a comparison of Xe-derivatized and inhibitor-bound X-ray crystal structures in dehaloperoxidase-hemoglobin (DHP A) of Amphitrite ornata. The internal binding affinity of four different inhibitors, 4-fluorophenol, 4-chlorophenol, 4-bromophenol, and 4-iodophenol in the distal pocket has been shown previously to increase proportional to the radius of the para-halogen atom. Inhibition of oxidation of the native substrate, 2,4,6-tribromophenol, has been shown to follow the trend in inhibitor binding strength, because of a two-site competitive inhibition mechanism that involves displacement of the substrate by the inhibitor in a gated mechanism involving the distal histidine of DHP A. In this study, it is shown that the origin of the stronger binding by a larger para-halogen substituent coincides structurally with a Xe-binding cavity (Xe1) characterized structurally by X-ray crystallography. The Xe1 site is surrounded by amino acid resides L100, F21, F24, F35, F60, and V59 in the distal pocket, located 4.8 angstrom from the heme iron, in a position that is coincident with the para-bromine atom of the inhibitor 4-bromophenol. 4-bromophenol is prevalent in benthic ecosystems where A. ornata resides. A second, less well-defined, binding site in DHP A, labeled as Xe2, is located near the surface of the protein in the vicinity of amino acid residues L62, R69, D79, T82, and L83, which may be related to substrate docking on the surface of DHP A. (c) 2011 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 98: 2735, 2012.