Zeng J, Fenna R E
Department of Biochemistry and Molecular Biology, University of Miami Medical School, FL 33101.
J Mol Biol. 1992 Jul 5;226(1):185-207. doi: 10.1016/0022-2836(92)90133-5.
The three-dimensional structure of the enzyme myeloperoxidase has been determined by X-ray crystallography to 3 A resolution. Two heavy atom derivatives were used to phase an initial multiple isomorphous replacement map that was subsequently improved by solvent flattening and non-crystallographic symmetry averaging. Crystallographic refinement gave a final model with an R-factor of 0.257. The root-mean-square deviations from ideality for bond lengths and angles were 0.011 A and 3.8 degrees. Two, apparently identical, halves of the molecule are related by local dyad and covalently linked by a single disulfide bridge. Each half-molecule consists of two polypeptide chains of 108 and 466 amino acid residues, a heme prosthetic group, a bound calcium ion and at least three sites of asparagine-linked glycosylation. There are six additional intra-chain disulfide bonds, five in the large polypeptide and one in the small. A central core region that includes the heme binding site is composed of five alpha-helices. Regions of the larger polypeptide surrounding this core are organized into locally folded domains in which the secondary structure is predominantly alpha-helical with very little organized beta-sheet. A proximal ligand to the heme iron atom has been identified as histidine 336, which is in turn hydrogen-bonded to asparagine 421. On the distal side of the heme, histidine 95 and arginine 239 are likely to participate directly in the catalytic mechanism, in a manner analogous to the distal histidine and arginine of the non-homologous enzyme cytochrome c peroxidase. The site of the covalent linkage to the heme has been tentatively identified as glutamate 242, although the chemical nature of the link remains uncertain. The calcium binding site has been located in a loop comprising residues 168 to 174 together with aspartate 96. Myeloperoxidase is a member of a family of homologous mammalian peroxidases that includes thyroid peroxidase, eosinophil peroxidase and lactoperoxidase. The heme environment, defined by our model for myeloperoxidase, appears to be highly conserved in these four mammalian peroxidases. Furthermore, the conservation of all 12 cysteine residues involved in the six intra-chain disulfide bonds and the calcium binding loop suggests that the three-dimensional structures of members of this gene family are likely to be quite similar.
通过X射线晶体学已确定髓过氧化物酶的三维结构，分辨率达3埃。使用两种重原子衍生物对初始多重同晶置换图谱进行相位确定，随后通过溶剂扁平化和非晶体学对称性平均对其进行改进。晶体学精修得到了一个最终模型，其R因子为0.257。键长和键角与理想值的均方根偏差分别为0.011埃和3.8度。分子的两个明显相同的部分通过局部二元对称相关，并通过一个二硫键共价连接。每个半分子由两条分别含有108个和466个氨基酸残基的多肽链、一个血红素辅基、一个结合的钙离子以及至少三个天冬酰胺连接的糖基化位点组成。还有六个链内二硫键，其中五个在大的多肽链中，一个在小的多肽链中。包括血红素结合位点的中央核心区域由五个α螺旋组成。围绕该核心的较大多肽区域被组织成局部折叠结构域，其中二级结构主要为α螺旋，几乎没有有组织的β折叠片层。已确定血红素铁原子的近端配体为组氨酸336，其又与天冬酰胺421形成氢键。在血红素的远端，组氨酸95和精氨酸239可能以类似于非同源酶细胞色素c过氧化物酶的远端组氨酸和精氨酸的方式直接参与催化机制。与血红素共价连接的位点已初步确定为谷氨酸242，尽管连接的化学性质仍不确定。钙结合位点位于包含残基168至174以及天冬氨酸96的环中。髓过氧化物酶是同源哺乳动物过氧化物酶家族的成员，该家族包括甲状腺过氧化物酶、嗜酸性粒细胞过氧化物酶和乳过氧化物酶。由我们的髓过氧化物酶模型所定义的血红素环境在这四种哺乳动物过氧化物酶中似乎高度保守。此外，参与六个链内二硫键和钙结合环的所有12个半胱氨酸残基的保守性表明，该基因家族成员的三维结构可能非常相似。
