Hasan Rajnee, Rony Md Nazmul Haq, Ahmed Rasel
Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Manik Mia Avenue, Dhaka, 1207, Bangladesh.
J Genet Eng Biotechnol. 2021 Feb 2;19(1):25. doi: 10.1186/s43141-020-00105-y.
The M4 family of metalloproteases is comprised of a large number of zinc-containing metalloproteases. A large number of these enzymes are important virulence factors of pathogenic bacteria and therefore potential drug targets. Whereas some enzymes have potential for biotechnological applications, the M4 family of metalloproteases is known almost exclusively from bacteria. The aim of the study was to identify the structure and properties of M4 metalloprotease proteins.
A total of 31 protein sequences of M4 metalloprotease retrieved from UniProt representing different species of bacteria have been characterized for various physiochemical properties. They were thermostable, hydrophillic protein of a molecular mass ranging from 38 to 66 KDa. Correlation on the basis of both enzymes and respective genes has also been studied by phylogenetic tree. B. cereus M4 metalloprotease (PDB ID: 1NPC) was selected as a representative species for secondary and tertiary structures among the M4 metalloprotease proteins. The secondary structure displaying 11 helices (H1-H11) is involved in 15 helix-helix interactions, while 4 β-sheet motifs composed of 15 β-strands in PDBsum. Possible disulfide bridges were absent in most of the cases. The tertiary structure of B. cereus M4 metalloprotease was validated by QMEAN4 and SAVES server (Ramachandran plot, verify 3D, and ERRAT) which proved the stability, reliability, and consistency of the tertiary structure of the protein. Functional analysis was done in terms of membrane protein topology, disease-causing region prediction, proteolytic cleavage sites prediction, and network generation. Transmembrane helix prediction showed absence of transmembrane helix in protein. Protein-protein interaction networks demonstrated that bacillolysin of B. cereus interacted with ten other proteins in a high confidence score. Five disorder regions were identified. Active sites analysis showed the zinc-binding residues-His-143, His-147, and Glu-167, with Glu-144 acting as the catalytic residues.
Moreover, this theoretical overview will help researchers to get a details idea about the protein structure and it may also help to design enzymes with desirable characteristics for exploiting them at industrial level or potential drug targets.
金属蛋白酶M4家族由大量含锌金属蛋白酶组成。这些酶中有许多是病原菌的重要毒力因子，因此是潜在的药物靶点。虽然有些酶具有生物技术应用潜力，但金属蛋白酶M4家族几乎仅在细菌中为人所知。本研究的目的是确定M4金属蛋白酶蛋白的结构和特性。
从UniProt检索到的代表不同细菌物种的31条M4金属蛋白酶蛋白序列已针对各种理化性质进行了表征。它们是热稳定的亲水性蛋白，分子量在38至66 kDa之间。还通过系统发育树研究了基于酶和各自基因的相关性。蜡样芽孢杆菌M4金属蛋白酶（PDB ID：1NPC）被选为M4金属蛋白酶蛋白中二级和三级结构的代表性物种。二级结构显示11个螺旋（H1-H11）参与15个螺旋-螺旋相互作用，而在PDBsum中由15条β链组成4个β折叠基序。大多数情况下不存在可能的二硫键。蜡样芽孢杆菌M4金属蛋白酶的三级结构通过QMEAN4和SAVES服务器（拉氏图、Verify 3D和ERRAT）进行了验证，这证明了该蛋白三级结构的稳定性、可靠性和一致性。从膜蛋白拓扑结构、致病区域预测、蛋白水解切割位点预测和网络生成方面进行了功能分析。跨膜螺旋预测显示该蛋白中不存在跨膜螺旋。蛋白质-蛋白质相互作用网络表明，蜡样芽孢杆菌的芽孢溶素与其他十种蛋白质以高置信度得分相互作用。鉴定出五个无序区域。活性位点分析显示锌结合残基为His-143、His-147和Glu-167，Glu-144作为催化残基。
此外，这一理论概述将有助于研究人员详细了解该蛋白结构，也可能有助于设计具有理想特性的酶，以便在工业层面加以利用或作为潜在的药物靶点。
