@article { ISI:000239324300008, title = {Conformation and microenvironment of the active site of a low molecular weight 1,4-beta-D-glucan glucanohydrolase from an alkalothermophilic thermomonospora sp.: involvement of lysine and cysteine residues}, journal = {Biochemical and Biophysical Research Communications}, volume = {347}, number = {2}, year = {2006}, month = {AUG}, pages = {428-432}, publisher = {ACADEMIC PRESS INC ELSEVIER SCIENCE}, type = {Article}, address = {525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA}, abstract = {

Conformation and microenvironment at the active site of 1,4-beta-D-glucan glucanohydrolase was probed with fluorescent chemo-affinity labeling using o-phthalaldehyde. OPTA has been known to form a fluorescent isoindole derivative by cross-linking the proximal thiol and amino groups of cysteine and lysine. Modification of lysine of the enzyme by TNBS and of cysteine residue by PHMB abolished the ability of the enzyme to form an isoindole derivative with OPTA. Kinetic analysis of the TNBS and PHMB-modified enzyme suggested the presence of essential lysine and cysteine residues, respectively, at the active site of the enzyme. The substrate protection of the enzyme with carboxymethylcellulose (CMC) confirmed the involvement of lysine and cysteine residues in the active site of the enzyme. Multiple sequence alignment of peptides obtained by tryptic digestion of the enzyme showed cysteine is one of the conserved amino acids corroborating the chemical modification studies. (c) 2006 Elsevier Inc. All rights reserved.

}, keywords = {1, 4-beta-D-glucan glucanohydrolase, active site microenvironment, Cysteine, lysine, OPTA, PHMB, Thermomonospora sp., TNBS}, issn = {0006-291X}, doi = {10.1016/j.bbrc.2006.06.100}, author = {Jagtap, Sharmili and Rao, Mala} } @article { ISI:000245519000047, title = {Active site directed chemical modification of alpha-galactosidase from bacillus stearothermophilus (NCIM 5146): involvement of lysine, tryptophan and carboxylate residues in catalytic site}, journal = {Enzyme and Microbial Technology}, volume = {40}, number = {5}, year = {2007}, month = {APR}, pages = {1312-1320}, publisher = {ELSEVIER SCIENCE INC}, type = {Article}, address = {360 PARK AVE SOUTH, NEW YORK, NY 10010-1710 USA}, abstract = {

The catalytic amino acid residues of the extracellular a-galactosidase (alpha-D-galactoside galactohydrolase; EC 3.2.1.22) from Bacillus stearothermophilus NCIM 5146 were investigated by pH dependence and chemical modification studies. These results suggested that carboxylate and a lysine residue take part in catalysis and only lysine residues were essential for substrate binding. Carbodiimide mediated chemical modification of the enzyme also supported that a carboxylate residue located in the active site act as a nucleophile base in substrate cleavage. Acylation and reductive methylation of lysine residues by acetic, citraconic anhydride and sodium borohydride suggested that four protonated lysine residues carrying positive charge on its epsilon-amino group provides the positive charge density for binding of the substrate. Additionally four tryptophan residues also found near to the active site and in a moderately hydrophobic environment. Kinetic and thermal inactivation study of modified enzyme indicated that these tryptophan residues might have a role in the catalytic site as well as in the thermal stabilization of active site conformation at higher temperature. (c) 2006 Elsevier Inc. All rights reserved.

}, keywords = {Active site, alpha-galactosidase, Bacillus stearothermophilus, carboxylate, Chemical modification, lysine, Tryptophan}, issn = {0141-0229}, doi = {10.1016/j.enzmictec.2006.10.004}, author = {Gote, M. M. and Khan, Mohammad Islam and Khire, Jayant Malhar} } @article {46671, title = {Biological process of lysine-tRNA charging is therapeutically targetable in liver cancer}, journal = {Liver International}, volume = {41}, year = {2021}, month = {JAN }, pages = {206-219}, type = {Article }, abstract = {

Background \& Aims Mature transfer RNAs (tRNA) charged with amino acids decode mRNA to synthesize proteins. Dysregulation of translational machineries has a fundamental impact on cancer biology. This study aims to map the tRNAome landscape in liver cancer patients and to explore potential therapeutic targets at the interface of charging amino acid with tRNA. Methods Resected tumour and paired tumour-free (TFL) tissues from hepatocellular carcinoma (HCC) patients (n = 69), and healthy liver tissues from organ transplant donors (n = 21), HCC cell lines, and cholangiocarcinoma (CC) patient-derived tumour organoids were used. Results The expression levels of different mature tRNAs were highly correlated and closely clustered within individual tissues, suggesting that different members of the tRNAome function cooperatively in protein translation. Interestingly, high expression of tRNA-Lys-CUU in HCC tumours was associated with more tumour recurrence (HR 1.1;P = .022) and worse patient survival (HR 1.1;P = .0037). The expression of Lysyl-tRNA Synthetase (KARS), the enzyme catalysing the charge of lysine to tRNA-Lys-CUU, was significantly upregulated in HCC tumour tissues compared to tumour-free liver tissues. In HCC cell lines, lysine deprivation, KARS knockdown or treatment with the KARS inhibitor cladosporin effectively inhibited overall cell growth, single cell-based colony formation and cell migration. This was mechanistically mediated by cell cycling arrest and induction of apoptosis. Finally, these inhibitory effects were confirmed in 3D cultured patient-derived CC organoids. Conclusions The biological process of charging tRNA-Lys-CUU with lysine sustains liver cancer cell growth and migration, and is clinically relevant in HCC patients. This process can be therapeutically targeted and represents an unexplored territory for developing novel treatment strategies against liver cancer.

}, keywords = {Cladosporin, liver cancer, lysine, Lysyl-tRNA Synthetase, tRNA-Lys-CUU, tRNAome}, issn = {1478-3223}, doi = {10.1111/liv.14692}, author = {Zhang, Ruyi and Noordam, Lisanne and Ou, Xumin and Ma, Buyun and Li, Yunlong and Das, Pronay and Shi, Shaojun and Liu, Jiaye and Wang, Ling and Li, Pengfei and Verstegen, Monique M. A. and Reddy, D. Srinivasa and van Der Laan, Luc J. W. and Peppelenbosch, Maikel P. and Kwekkeboom, Jaap and Smits, Ron and Pan, Qiuwei} }