Schacherl Magdalena, Montada Angelika A M, Brunstein Elena, Baumann Ulrich
Department of Chemistry, Institute of Biochemistry, University of Cologne, Otto-Fischer-Strasse 12-14, D-50674 Cologne, Germany.
Acta Crystallogr D Biol Crystallogr. 2015 Dec 1;71(Pt 12):2505-12. doi: 10.1107/S1399004715019549. Epub 2015 Nov 27.
The U32 family is a collection of over 2500 annotated peptidases in the MEROPS database with unknown catalytic mechanism. They mainly occur in bacteria and archaea, but a few representatives have also been identified in eukarya. Many of the U32 members have been linked to pathogenicity, such as proteins from Helicobacter and Salmonella. The first crystal structure analysis of a U32 catalytic domain from Methanopyrus kandleri (gene mk0906) reveals a modified (βα)8 TIM-barrel fold with some unique features. The connecting segment between strands β7 and β8 is extended and helix α7 is located on top of the C-terminal end of the barrel body. The protein exhibits a dimeric quaternary structure in which a zinc ion is symmetrically bound by histidine and cysteine side chains from both monomers. These residues reside in conserved sequence motifs. No typical proteolytic motifs are discernible in the three-dimensional structure, and biochemical assays failed to demonstrate proteolytic activity. A tunnel in which an acetate ion is bound is located in the C-terminal part of the β-barrel. Two hydrophobic grooves lead to a tunnel at the C-terminal end of the barrel in which an acetate ion is bound. One of the grooves binds to a Strep-Tag II of another dimer in the crystal lattice. Thus, these grooves may be binding sites for hydrophobic peptides or other ligands.
U32家族是MEROPS数据库中2500多种注释肽酶的集合，其催化机制未知。它们主要存在于细菌和古生菌中，但在真核生物中也鉴定出了一些代表成员。许多U32成员与致病性有关，例如来自幽门螺杆菌和沙门氏菌的蛋白质。对来自坎氏甲烷嗜热菌（基因mk0906）的U32催化结构域进行的首次晶体结构分析揭示了一种具有一些独特特征的修饰（βα）8 TIM桶状折叠。β7和β8链之间的连接段延伸，α7螺旋位于桶状体C末端的顶部。该蛋白质呈现二聚体四级结构，其中锌离子由来自两个单体的组氨酸和半胱氨酸侧链对称结合。这些残基存在于保守的序列基序中。在三维结构中没有可识别的典型蛋白水解基序，生化分析也未能证明其蛋白水解活性。在β桶的C末端部分有一个结合乙酸根离子的通道。两条疏水凹槽通向桶状结构C末端的一个通道，其中结合有一个乙酸根离子。其中一条凹槽与晶格中另一个二聚体的链霉亲和素标签II结合。因此，这些凹槽可能是疏水肽或其他配体的结合位点。
