Structural Research of Membrane-Bound Metalloproteases
Membrane-bound metalloproteases have various functions such as protein hydrolysis, degradation and remodeling of extracellular matrix, and intracellular signal transduction. Most of them contain zinc-bound metalloprotease domains. By regulating signal transduction and tumor microenvironment, it participates in pathological processes including tumor occurrence, development, invasion, and metastasis. Therefore, deeper research into the function of membrane-bound metalloproteases in cancer immune regulation will help develop cancer diagnosis and immunotherapy methods.
Structure and action mechanism of Escherichia coli zinc metalloprotease RseP
RseP from Escherichia coli is a zinc metalloprotease site 2 protease (S2P) homolog. It participates in the second step of signal transduction by sequentially cleaving type II membrane proteins. The Ec RseP structure contains three C-terminal residues. TM1 contains two zinc coordination His residues. TM3 is divided into two segments by a circular protrusion. Ec RseP is expected to have two inner membranes β Hairpin (the C1N loop and MREβ-loop), located between TM1 and TM2.
Figure 1. Two views of the full-length Ec RseP structure. (Yuki Imaizumi, et al., 2022)
Structure Mycobacterium tuberculosis M13 metalloprotease Zmp1
Zmp1 is a type II transmembrane protein with a short N-terminal intracellular structural domain, a transmembrane helix, and a protease structural domain localized in extracellular or intracellular vesicles. It has D1 and D2 structural domains, both consisting of helices. Two open-state cryo-EM structures of Zmp1 have been reported at 3.1 Å and 4.6 Å resolution, and the dominant state in solution is revealed by SAXS analysis.
Figure 2. Cryo-EM maps of Zmp1. (Liang WG, et al., 2021)
| Protein | Organism | Method | Resolution | PDB Entry ID |
| PRO form of proMMP-7 in complex with zwitterionic membrane | Homo sapiens | SOLUTION NMR | / | 2MZH |
| PRO form of proMMP-7 in complex with anionic membrane | Homo sapiens | SOLUTION NMR | / | 2MZI |
| M1 zinc metallopeptidase E323A mutant | Deinococcus radiodurans R1 | X-ray diffraction | 1.83 Å | 6IFF |
| M1 zinc metallopeptidase E323A mutant bound to Tyr-ser-ala substrate | Deinococcus radiodurans R1 | X-ray diffraction | 1.9 Å | 6IFG |
| Two domain M1 Zinc metallopeptidase E323A mutant bound to L-tryptophan amino acid | Deinococcus radiodurans R1 | X-ray diffraction | 2.35 Å | 6KOY |
| Partial open state of zinc metalloprotease 1 | Mycobacterium tuberculosis H37Rv | X-ray diffraction | 4.6 Å | 7K1V |
| RseP orthologue in complex with batimastat in space group P21 | Kangiella koreensis DSM 16069 | X-ray diffraction | 3.15 Å | 7W6Z |
| PDZ-C domain fragment of RseP orthologue | Kangiella koreensis DSM 16069 | X-ray diffraction | 1.15 Å | 7W70 |
| Zinc metalloprotease zmp1 in open state | Mycobacterium tuberculosis H37Rv | X-ray diffraction | 3.1 Å | 6XLY |
| Insulin-regulated aminopeptidase with alanine in active site | Homo sapiens | X-ray diffraction | 3.02 Å | 4P8Q |
| Insulin-regulated aminopeptidase with lysine in active site | Homo sapiens | X-ray diffraction | 2.96 Å | 4PJ6 |
| Insulin-regulated aminopeptidase in complex with ligand | Homo sapiens | X-ray diffraction | 3.31 Å | 4Z7I |
| Insulin regulated aminopeptidase | Homo sapiens | X-ray diffraction | 3.37 Å | 5C97 |
| Insulin-regulated aminopeptidase complexed with a macrocyclic peptidic inhibitor | Homo sapiens | X-ray diffraction | 3.2 Å | 6YDX |
| Aminopeptidase N | Escherichia coli | X-ray diffraction | 1.5 Å | 2DQ6 |
| Aminopeptidase N complexed with bestatin | Escherichia coli | X-ray diffraction | 1.6 Å | 2DQM |
| Aminopeptidase N | Neisseria meningitidis MC58 | X-ray diffraction | 2.05 Å | 2GTQ |
| PepN (Aminopeptidase N)in complex with Bestatin | Escherichia coli K-12 | X-ray diffraction | 2.3 Å | 2HPT |
| Aminopeptidase N in complex with arginine | Escherichia coli K-12 | X-ray diffraction | 2 Å | 3B2P |
| Aminopeptidase N in complex with Lysine | Escherichia coli | X-ray diffraction | 1.5 Å | 3B2X |
Table 1. Structural research of membrane-bound metalloproteases.
To study the structure of membrane proteins, we use NMR spectroscopy, cryo-electron microscopy (cryo-EM) and X-ray crystallography. Structural analysis of membrane-bound metalloproteases contributes to the development of novel antimicrobial targets and cancer therapies.
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References
- Yuki Imaizumi, et al. Mechanistic insights into intramembrane proteolysis by E. coli site-2 protease homolog RseP. Sci. Adv. 2022. 8, eabp9011.
- Liang WG, et al. Structural analysis of Mycobacterium tuberculosis M13 metalloprotease Zmp1 open states. Structure. 2021. 29(7):709-720.
