Meinnel T, Blanquet S, Dardel F
Laboratoire de Biochimie URA 1970 du Centre National de la Recherche Scientifique, Ecole Polytechnique, Palaiseau, France.
J Mol Biol. 1996 Sep 27;262(3):375-86. doi: 10.1006/jmbi.1996.0521.
Escherichia coli peptide deformylase, a member of the zinc metalloproteases family, is made up of an active core domain composed of 147 residues and of an additional and dispensable C-terminal tail of 21 residues. The three-dimensional structure of the catalytic core could be studied by NMR. 1H and 15N NMR resonances assignments were obtained by two-dimensional and three-dimensional heteronuclear spectroscopy. The structure could be calculated using a set of 1015 restraints for the 147 residues of the enzyme. The overall structure is composed of a series of antiparallel beta-strands which surround two perpendicular alpha-helices. The C-terminal helix contains the HEXXH motif, which is crucial for activity. This helical arrangement and the way the histidines bind the zinc ion clearly are structurally reminiscent of the other members of the metalloprotease family, such as thermolysin or metzincins. Nevertheless, the overall arrangement of secondary and tertiary structures of peptide deformylase and the positioning of its third zinc ligand (a cysteine) are quite different from those of the other members of the family. These discrepancies, together with several biochemical differences, lead us to propose that peptide deformylase is the first example of a new class of the zinc-metalloproteases family. Studies of the interaction of peptide deformylase with either an inhibitor of the reaction or a product of the catalysed reaction, Met-Ala-Ser, as well as comparisons with the structures of other enzymes of the family, have enabled us to delineate the area corresponding to their binding site. The structural basis of the specificity of recognition of the formyl group is discussed in the context of the protease superfamily.
大肠杆菌肽脱甲酰基酶是锌金属蛋白酶家族的一员，由一个由147个残基组成的活性核心结构域和一个额外的、可有可无的21个残基的C末端尾巴组成。催化核心的三维结构可以通过核磁共振进行研究。通过二维和三维异核光谱获得了1H和15N核磁共振共振归属。可以使用针对该酶147个残基的一组1015个约束来计算结构。整体结构由一系列围绕两个垂直α螺旋的反平行β链组成。C末端螺旋包含HEXXH基序，这对活性至关重要。这种螺旋排列以及组氨酸结合锌离子的方式在结构上明显让人联想到金属蛋白酶家族的其他成员，如嗜热菌蛋白酶或金属锌蛋白酶。然而，肽脱甲酰基酶二级和三级结构的整体排列及其第三个锌配体（半胱氨酸）的定位与该家族的其他成员有很大不同。这些差异，连同一些生化差异，使我们提出肽脱甲酰基酶是锌金属蛋白酶家族新一类的第一个例子。对肽脱甲酰基酶与反应抑制剂或催化反应产物Met-Ala-Ser相互作用的研究，以及与该家族其他酶结构的比较，使我们能够勾勒出与其结合位点相对应的区域。在蛋白酶超家族的背景下讨论了甲酰基识别特异性的结构基础。
