Huang D B, Chang C H, Ainsworth C, Brünger A T, Eulitz M, Solomon A, Stevens F J, Schiffer M
Center for Mechanistic Biology and Biotechnology, Argonne National Laboratory, Illinois 60439-4833.
Biochemistry. 1994 Dec 13;33(49):14848-57. doi: 10.1021/bi00253a024.
The sequence and structure of a second human kappa 1 immunoglobulin light-chain variable domain, Wat, has been determined. The R-factor is 15.7% for 1.9-A data. One hundred and ninety-five water molecules were identified; 30 water molecules were located in identical positions in each of the monomers. Some of the water molecules are integral parts of the domains. This light chain is encoded by the same variable domain gene that encoded the previously characterized kappa I variable domain, Rei. Due to limited somatic mutation, the two highly homologous proteins differ in only 20 of the 108 residues. Wat crystallized in space group P6(4) while Rei crystallized in space group P6(1); in both crystals, the asymmetric unit was the noncovalent dimer. Although the basic domain structure is the same for both proteins, the relative positions of the domains within the two dimers differ. This difference is most likely accounted for by the replacement of Tyr36 in Rei by Phe in the Wat protein. Residue Tyr36 is part of the hydrogen-bonding network in the interface between the domains in Rei. Losing the hydrogen-bonding capability of residue 36 by replacement of Tyr by Phe alters the network of hydrogen bonds between the domains, resulting in a different domain-domain contact. The details of lattice contacts in the two crystals were compared. One type of contact that extends the beta-sheet of the individual domains was conserved, but because it involved different symmetry elements within the crystal, different crystal packing resulted. In the Wat crystal, one of the contacts shows an example of how a symmetrical binding site can "bind" an asymmetrical object. Further, the examination of the Wat crystal also illustrates how the different crystalline environments of the domains of the dimer results in different distributions of temperature factors for the residues within the domains.
已确定了第二种人类κ1免疫球蛋白轻链可变结构域Wat的序列和结构。对于1.9埃的数据，R因子为15.7%。鉴定出195个水分子；30个水分子位于每个单体的相同位置。一些水分子是结构域的组成部分。这条轻链由与先前表征的κI可变结构域Rei相同的可变结构域基因编码。由于体细胞突变有限，这两种高度同源的蛋白质在108个残基中只有20个不同。Wat在空间群P6(4)中结晶，而Rei在空间群P6(1)中结晶；在这两种晶体中，不对称单元都是非共价二聚体。虽然这两种蛋白质的基本结构域结构相同，但两个二聚体内结构域的相对位置不同。这种差异很可能是由于Wat蛋白中用苯丙氨酸取代了Rei中的酪氨酸36。残基酪氨酸36是Rei中结构域间界面氢键网络的一部分。用苯丙氨酸取代酪氨酸导致残基36失去氢键结合能力，改变了结构域间的氢键网络，从而导致不同的结构域-结构域接触。比较了两种晶体中晶格接触的细节。一种延伸单个结构域β折叠的接触是保守的，但由于它涉及晶体内不同的对称元素，导致了不同的晶体堆积。在Wat晶体中，其中一种接触展示了一个对称结合位点如何“结合”一个不对称物体的例子。此外，对Wat晶体的研究还说明了二聚体结构域的不同晶体环境如何导致结构域内残基温度因子的不同分布。
