STRUCTURAL DETAILS OF RIBONUCLEASE-H FROM ESCHERICHIA-COLI AS REFINED TO AN ATOMIC RESOLUTION
STRUCTURAL DETAILS OF RIBONUCLEASE-H FROM ESCHERICHIA-COLI AS REFINED TO AN ATOMIC RESOLUTION
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DOI：
10.1016/0022-2836(92)90260-q
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发表时间：
1992-02-20
影响因子：
5.6
通讯作者：
MORIKAWA, K
中科院分区：
文献类型：
--
作者：
KATAYANAGI, K;MIYAGAWA, M;MORIKAWA, K
本文用多重同晶置换法测定了大肠杆菌RNase H的晶体结构，并用立体化学约束最小二乘法修正了晶体结构，在1.48 μ m分辨率下，晶体学R因子为0.196。在最终结构中，均方根（r.m.s.）粘合长度的偏差为0.017 mm，角距离的偏差为0.036 mm。该结构由一个五链β-折叠和五个α-螺旋组成，并揭示了分子内和分子间残基之间氢键，静电和疏水相互作用的细节。精细的结构允许解释由螺旋αIII和随后的环组成的基本突起与其余主要结构域之间的特定相互作用。β折叠、αII、αIII和αIV形成一个中央疏水裂缝，包含所有6个色氨酸残基，并可能用于固定基本突起的方向。两个平行相邻的螺旋，αI和αIV，与一些疏水相互作用的三联体相关，包括许多亮氨酸残基，这些残基与重复的亮氨酸基序相似。定义明确的电子密度图允许详细讨论可能参与结合DNA/RNA杂交体的氨基酸残基，以及构建与DNA/RNA杂交体寡聚体复合的酶的推定模型。在该模型中，从Mg 2+结合位点到基本突起的蛋白质区域大致覆盖了DNA/RNA杂交双螺旋的两个转角。含有6个甘氨酸残基的片段（11-23）在βA和βB链之间形成一个长环。这个突出到溶剂区域的环位于复合物模型中酶与DNA/RNA杂交体之间的界面上。主链原子的平均温度因子在构成基本突起的螺旋αIII中显示出显著的高值，表明其柔性与核酸结合功能之间存在一定的相关性。的Mg 2+结合位点，周围的四个不变的酸性残基，现在可以更精确地描述与催化活性。晶体内的分子的排列似乎是占主导地位的抵消了显着偏置的电荷分布在分子表面上，这是来自特别是从酸性Mg 2+结合位点和碱性突起之间的分离。
The crystal structure of RNase H fromEscherichia colihas been determined by the multiple isomorphous replacement method, and refined by the stereochemically restrained leastsquares procedure to a crystallographicR-factor of 0.196 at 1.48 Å resolution. In the final structure, the root-mean-square (r.m.s.) deviation for bond lengths is 0.017 Å, and for angle distances 0.036 Å. The structure is composed of a five-stranded β-sheet and five α-helices, and reveals the details of hydrogen bonding, electrostatic and hydrophobic interactions between intra- and intermolecular residues. The refined structure allows an explanation of the particular interactions between the basic protrusion, consisting of helix αIII and the following loop, and the remaining major domain. The β-sheet, αII, αIII and αIV form a central hydrophobic cleft that contains all six tryptophan residues, and presumably serves to fix the orientation of the basic protrusion. Two parallel adjacent helices, αI and αIV, are associated with a few triads of hydrophobic interactions, including many leucine residues, that are similar to the repeated leucine motif. The well-defined electron density map allows detailed discussion of amino acid residues likely to be involved in binding a DNA/RNA hybrid, and construction of a putative model of the enzyme complexed with a DNA/RNA hybrid oligomer. In this model, a protein region, from the Mg2+-binding site to the basic protrusion, covers roughly two turns of a DNA/RNA hybrid double helix. A segment (11–23) containing six glycine residues forms a long loop between the βA and βB strands. This loop, which protrudes into the solvent region, lies on the interface between the enzyme and a DNA/RNA hybrid in the model of the complex. The mean temperature factors of main-chain atoms show remarkably high values in helix αIII that constitutes the basic protrusion, suggesting some correlation between its flexibility and the nucleic acid binding function. The Mg2+-binding site, surrounded by four invariant acidic residues, can now be described more precisely in conjunction with the catalytic activity. The arrangement of molecules within the crystal appears to be dominated by the cancelling out of a remarkably biased charge distribution on the molecular surface, which is derived in particular from the separation between the acidic Mg2+-binding site and the basic protrusion.