Crystallographic structure of a PLP-dependent ornithine decarboxylase from Lactobacillus 30a to 3.0 A resolution.
Crystallographic structure of a PLP-dependent ornithine decarboxylase from Lactobacillus 30a to 3.0 A resolution.
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DOI：
10.1006/jmbi.1995.0526
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发表时间：
1995-10
影响因子：
5.6
通讯作者：
C. Momany;C. Momany;S. Ernst;R. Ghosh;N. Chang;M. Hackert
中科院分区：
文献类型：
--
作者：
C. Momany;C. Momany;S. Ernst;R. Ghosh;N. Chang;M. Hackert
来自乳杆菌30 a的鸟氨酸脱羧酶（L30 a OrnDC）是作用于赖氨酸、精氨酸或鸟氨酸的大的吡哆醛-5 '-磷酸依赖性脱羧酶的代表。L30 a OrnDC的晶体结构已经使用MIR相结合密度修正（空间群P6; a = 195.6 A，c = 97.6 A; 1460个氨基酸残基/不对称单元的二聚体; VM = 3.26 A3/Da）解析至3.0 A分辨率。使用2倍限制、4 sigma截止值和8.0至3.0 A分辨率数据，精确的晶体学R值为0.219（Rfree = 0.268）。由C6对称性相关的六个二聚体组成酶活性十二聚体（约10（6）Da）。L30 a OrnDC的每个单体可以用五个连续折叠结构域来描述。氨基末端结构域（残基1至107）由称为“翼”结构域的五链β折叠组成。每个二聚体的两个翼结构域向内朝向十二聚体的中心突出，并有助于十二聚体稳定化。“接头”结构域，残基108至160，由短α-螺旋组成，所述短α-螺旋由填充PLP口袋的环分开。第三个结构域，残基161至413，是含有类似于天冬氨酸转氨酶的PLP结合结构域的七链β折叠的α/β结构域。第四个结构域，残基414至569，类似于天冬氨酸转氨酶的“小”结构域，但由于插入而明显更大。剩余的羧基末端结构域，残基570至730，被组织成多个反平行环和七个α-螺旋，有助于形成通向PLP结合位点的深通道。
Ornithine decarboxylase from Lactobacillus 30a (L30a OrnDC) is representative of the large, pyridoxal-5'-phosphate-dependent decarboxylases that act on lysine, arginine or ornithine. The crystal structure of the L30a OrnDC has been solved to 3.0 A resolution using MIR phases in combination with density modification (space group P6; a = 195.6 A, c = 97.6 A; dimer of 1460 amino acid residues/asymmetric unit; VM = 3.26 A3/Da). The refined crystallographic R-value was 0.219 (Rfree = 0.268) using 2-fold restraints with a 4 sigma cutoff and 8.0 to 3.0 A resolution data. Six dimers related by C6 symmetry compose the enzymatically active dodecamer (approximately 10(6) Da). Each monomer of L30a OrnDC can be described in terms of five sequential folding domains. The amino-terminal domain, residues 1 to 107, consists of a five-stranded beta-sheet termed the "wing" domain. Two wing domains of each dimer project inward towards the center of the dodecamer and contribute to dodecamer stabilization. The "linker" domain, residues 108 to 160, consists of short alpha-helices separated by a loop that fills in the PLP pocket. The third domain, residues 161 to 413, is an alpha/beta domain containing a seven stranded beta-sheet that resembles the PLP-binding domain of the aspartate aminotransferases. The fourth domain, residues 414 to 569, resembles the "small" domain of the aspartate aminotransferases, but is significantly larger due to insertions. The remaining carboxy-terminal domain, residues 570 to 730, is organized into multiple antiparallel loops and seven alpha-helices that help form a deep channel leading to the PLP-binding site.