THE HIGH-RESOLUTION STRUCTURE OF THE PERIPHERAL SUBUNIT-BINDING DOMAIN OF DIHYDROLIPOAMIDE ACETYLTRANSFERASE FROM THE PYRUVATE-DEHYDROGENASE MULTIENZYME COMPLEX OF BACILLUS-STEAROTHERMOPHILUS
THE HIGH-RESOLUTION STRUCTURE OF THE PERIPHERAL SUBUNIT-BINDING DOMAIN OF DIHYDROLIPOAMIDE ACETYLTRANSFERASE FROM THE PYRUVATE-DEHYDROGENASE MULTIENZYME COMPLEX OF BACILLUS-STEAROTHERMOPHILUS
复制标题
DOI：
10.1006/jmbi.1993.1145
复制
发表时间：
1993-03-05
影响因子：
5.6
通讯作者：
PERHAM, RN
中科院分区：
文献类型：
--
作者：
KALIA, YN;BROCKLEHURST, SM;PERHAM, RN
三维结构的43个残基的活性，合成的肽，包括周边亚基结合结构域的二氢硫辛酰胺乙酰转移酶的丙酮酸脱氢酶多酶复合体的嗜热脂肪芽孢杆菌已确定通过多冷却动态模拟退火协议使用来自1H核磁共振波谱的限制。共使用了442个实验导出的约束，包括13个二面角（φ，χ1）约束。计算了最终一组35个结构，骨架原子与平均坐标的均方根偏差为0·36 μ π ι，当包括侧链重原子时，包含残基Val 7至Leu 39的明确定义的区域的均方根偏差为0·96 μ π ι。虽然进行了分配，并观察到N-末端6个残基和C-末端4个残基的连续连接性，但不存在长程NOE表明末端区域在很大程度上是非结构化的。结合结构域包含两个短的平行α-螺旋（残基Val 7至Lys 14和Lys 32至Leu 39）、一个310-螺旋（残基Asp 17至Val 21）和一个由重叠β-转角（残基Gln 22至Leu 31）组成的结构化环，其包围一个紧密堆积的疏水核心。Asp 34在很大程度上稳定了环。该残基在所有外周亚基结合结构域中是保守的，其羧酸酯侧链与Gly 23、Thr 24、Gly 25和Leu 31的主链酰胺质子形成一组侧链-主链氢键，并与Thr 24的羟基形成侧链-侧链氢键。我们提出，一个外围亚基结合位点可能位于环区，其中包含一系列高度保守的残基，并提供了一些潜在的识别位点。包含33个残基的结合结构域的结构化区域代表具有确定的三级结构的异常短的氨基酸序列，其没有二硫键、配体或辅因子来稳定折叠。它可能正在接近三维结构的尺寸下限，该三维结构具有较大结构的特征，包括紧密堆积的非极性内部。疏水核心中侧链的组织可能对新蛋白的设计具有福尔德意义。
The three-dimensional structure of a 43-residue active, synthetic peptide encompassing the peripheral subunit-binding domain of dihydrolipoamide acetyltransferase from the pyruvate dehydrogenase multienzyme complex ofBacillus stearothermophilushas been determined by means of a multi-cooling dynamical simulated annealing protocol using restraints derived from1H nuclear magnetic resonance spectroscopy. A total of 442 experimentally derived restraints including 13 dihedral angle (φ,χ1) restraints were used. A final set of 35 structures was calculated with a root-mean-square deviation from the mean co-ordinates of 0·36 Å for the backbone atoms and 0·96 Å when side-chain heavy atoms were included for the well-defined region comprising residues Val7 to Leu39. Although assignments were made and sequential connectivities observed for the N-terminal six and C-terminal four residues, the absence of long-range NOEs suggests that the terminal regions are largely unstructured. The binding domain contains two short parallel α-helices (residues Val7 to Lys14 and Lys32 to Leu39), a 310-helix (residues Asp17 to Val21) and a structured loop made up of overlapping β-turns (residues Gln22 to Leu31), which enclose a close-packed hydrophobic core. The loop is stabilized to a large extent by Asp34. This residue is conserved in all peripheral subunit-binding domains and its carboxylate side-chain forms a set of side-chain-main-chain hydrogen bonds with the main-chain amide protons of Gly23, Thr24, Gly25 and Leu31 and a side-chain-side-chain hydrogen bond with the hydroxyl group of Thr24. We propose that a peripheral subunit-binding site may be located in the loop region, which contains a series of highly conserved residues and provides a number of potential recognition sites. The structured region of the binding domain, comprising 33 residue, represents an exceptionally short amino acid sequence with defined tertiary structure that has no disulphide bond, ligand or cofactor to stabilize the fold. It may be approaching the lower size limit for a three-dimensional structure possessing features characteristic of larger structures, including a close-packed, non-polar interior. The organization of the side-chains in the hydrophobic core may have implications forde novoprotein design.