X-ray structure of the metcyano form of dehaloperoxidase from Amphitrite ornata: evidence for photoreductive dissociation of the iron-cyanide bond
X-ray structure of the metcyano form of dehaloperoxidase from Amphitrite ornata: evidence for photoreductive dissociation of the iron-cyanide bond
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DOI：
10.1107/s0907444910014605
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发表时间：
2010-07-01
影响因子：
2.2
通讯作者：
Franzen, S.
中科院分区：
文献类型：
--
作者：
de Serrano, V. S.;Davis, M. F.;Franzen, S.
为了进一步研究与血红素铁配位的双原子配体的几何构型，用同步辐射测定了脱氢过氧化物酶-血红蛋白(DHPCN)和DHPA的C73S突变体(C73SCN)的X射线晶体结构。用旋转阳极源测定了DHPCN的结构。这些结构表明，铁的光还原伴随着结合氰离子(CN-)的解离，这取决于X射线辐射的强度和曝光时间。电子密度与DHPCN远端口袋中两个位置的双原子分子的电子密度一致。然而，这两个位置的双原子配体的身份并不是唯一由电子密度图决定的。因此，用密度泛函理论计算确定了键长、键角和离解能是否与铁结合位上的CN-或O-2的键长、键角和离解能一致。此外，还进行了分子动力学模拟，以确定动力学是否与捕获在远端口袋第二位的CN-或O-2一致。基于这些计算以及与先前确定的DHP的C73S-O-2形式的X射线晶体结构的比较[De Serrano等人。(2007)，冰冻学报。D63,1094-1101]的结果表明，当晶体DHP在100K被光还原时，CN-逐渐被O-取代。DHP A的光还原容易与还原电位一致，但与其他过氧化物酶相比，DHPA有一种替代的激活机制，后者的还原电位通常为0.5V。Cn-在100K时的不稳定性表明，DHPA的远端口袋比大多数其他血红蛋白具有更大的灵活性。
X-ray crystal structures of the metcyano form of dehaloperoxidase- hemoglobin (DHP A) from Amphitrite ornata (DHPCN) and the C73S mutant of DHP A (C73SCN) were determined using synchrotron radiation in order to further investigate the geometry of diatomic ligands coordinated to the heme iron. The DHPCN structure was also determined using a rotating-anode source. The structures show evidence of photoreduction of the iron accompanied by dissociation of bound cyanide ion (CN-) that depend on the intensity of the X-ray radiation and the exposure time. The electron density is consistent with diatomic molecules located in two sites in the distal pocket of DHPCN. However, the identities of the diatomic ligands at these two sites are not uniquely determined by the electron-density map. Consequently, density functional theory calculations were conducted in order to determine whether the bond lengths, angles and dissociation energies are consistent with bound CN- or O-2 in the iron-bound site. In addition, molecular-dynamics simulations were carried out in order to determine whether the dynamics are consistent with trapped CN- or O-2 in the second site of the distal pocket. Based on these calculations and comparison with a previously determined X-ray crystal structure of the C73S-O-2 form of DHP [de Serrano et al. (2007), Acta Cryst. D63, 1094-1101], it is concluded that CN-is gradually replaced by O-2 as crystalline DHP is photoreduced at 100 K. The ease of photoreduction of DHP A is consistent with the reduction potential, but suggests an alternative activation mechanism for DHPA compared with other peroxidases, which typically have reduction potentials that are 0.5 V more negative. The lability of CN- at 100 K suggests that the distal pocket of DHPA has greater flexibility than most other hemoglobins.