Peptide name : Ribosome-inactivating protein lyophyllin (EC 3.2.2.22)

Source/Organism : Hon-shimeji

Linear/Cyclic : Not found

Chirality : Not found

Peptide length: 50

C-terminal modification: Not found

N-terminal modification : Free

Non-natural peptide information: None

Assay type : MTT assay

Assay time : 4h

Activity : IC50 : 489.8 μM

Cell line : HepG2

Cancer type : Not found

Other activity : Not found

Amino acid composition bar chart :

Molecular mass : 5358.0095 Dalton

Aliphatic index : 0.762

Instability index : 33.566

Hydrophobicity (GRAVY) : 0.096

Isoelectric point : 10.037

Charge (pH 7) : 2.7536

Aromaticity : 0.1

Molar extinction coefficient (cysteine, cystine): (6990, 6990)

Hydrophobic/hydrophilic ratio : 1.17391304

hydrophobic moment : -0.287

Missing amino acid : H,M,E

Most occurring amino acid : A

Most occurring amino acid frequency : 8

Least occurring amino acid : C

Least occurring amino acid frequency : 1

Secondary structure fraction (Helix, Turn, Sheet): (0.2, 0.2, 0.4)

SMILES Notation: CC[C@H](C)[C@H](N)C(=O)N[C@H](C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](CCC(N)=O)C(=O)NCC(=O)N[C@@H](CS)C(=O)N[C@@H](CO)C(=O)N1CCC[C@H]1C(=O)N[C@@H](C)C(=O)N[C@@H](CCCNC(=N)N)C(=O)N[C@@H](CCC(N)=O)C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@@H](CC(N)=O)C(=O)N[C@@H](C)C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@@H](CCCNC(=N)N)C(=O)N[C@@H](C)C(=O)N[C@@H](CCCNC(=N)N)C(=O)N[C@@H](C)C(=O)N[C@@H](CC(=O)O)C(=O)N[C@H](C(=O)N[C@@H](CCCNC(=N)N)C(=O)N[C@@H](C)C(=O)N[C@@H](C)C(=O)N[C@H](C(=O)N[C@@H](CO)C(=O)N[C@@H](C)C(=O)N[C@@H](CC(C)C)C(=O)N1CCC[C@H]1C(=O)N[C@H](C(=O)N[C@@H](CCCCN)C(=O)N[C@@H](C)C(=O)N1CCC[C@H]1C(=O)N[C@H](C(=O)N[C@@H](CO)C(=O)N[C@H](C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](CO)C(=O)N[C@H](C(=O)N[C@@H](Cc1c[nH]c2ccccc12)C(=O)N[C@@H](Cc1ccccc1)C(=O)NCC(=O)N[C@H](C(=O)N[C@@H](Cc1ccc(O)cc1)C(=O)N[C@@H](CC(N)=O)C(=O)N[C@@H](CC(=O)O)C(=O)O)C(C)C)[C@@H](C)O)[C@@H](C)O)C(C)C)[C@@H](C)O)C(C)C)C(C)C)[C@@H](C)O)[C@@H](C)CC)[C@@H](C)O)[C@@H](C)CC)C(C)C)[C@@H](C)O)[C@@H](C)O

1 : Lu JQ, et al. Lyophyllin, a Mushroom Protein from the Peptidase M35 Superfamily Is an RNA N-Glycosidase. Int J Mol Sci. 2021; 22:(unknown pages). doi: 10.3390/ijms222111598

Paper title : Lyophyllin, a Mushroom Protein from the Peptidase M35 Superfamily Is an RNA N-Glycosidase.

Doi : https://doi.org/10.3390/ijms222111598

Abstract : Ribosome-inactivating proteins (RIPs) hydrolyze the N-glycosidic bond and depurinate a specific adenine residue (A-4324 in rat 28S ribosomal RNA, rRNA) in the conserved α-sarcin/ricin loop (α-SRL) of rRNA. In this study, we have purified and characterized lyophyllin, an unconventional RIP from Lyophyllum shimeji, an edible mushroom. The protein resembles peptidase M35 domain of peptidyl-Lys metalloendopeptidases. Nevertheless, protein either from the mushroom or in recombinant form possessed N-glycosidase and protein synthesis inhibitory activities. A homology model of lyophyllin was constructed. It was found that the zinc binding pocket of this protein resembles the catalytic cleft of a classical RIP, with key amino acids that interact with the adenine substrate in the appropriate positions. Mutational studies showed that E122 may play a role in stabilizing the positively charged oxocarbenium ion and H121 for protonating N-3 of adenine. The tyrosine residues Y137 and Y104 may be used for stacking the target adenine ring. This work first shows a protein in the peptidase M35 superfamily based on conserved domain search possessing N-glycosidase activity.