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After destained, the gel pieces were reduced by incubation in a solution of 10 mM DTT at 60°C for 20 min，followed by alkylating in a solution of 25 mM iodacetamide（IAM）at room temperature for 15 min. The pieces were digested in-gel with trypsin (Promega, Madison, WI) overnight at 37°C. The produced peptides were extracted with 60% acetonitrile containing 5% formic acid and 100% acetonitrile successively, dried by SpeedVac, and was re-dissolved in 2% acetonitrile with 0.1% formic acid for LC-MS/MS analysis."],"repository":["Pride"],"modification":[""],"quantification_method":["Not available"],"data_protocol":["Tandem mass spectra were extracted, charge state deconvoluted and deisotoped by Compass Data Analysis version 4.1 (Bruker Daltonics). The peak list was directly generated from raw data using centroid algorithm with peak width set as 0.1 m/z and intensity above 100. No peak smooth or filter process was applied. After the charge states were calculated, the de-isotoped. peak list was exported as mgf file for further mascot search. Mascot (version 2.4, Matrix Science) was set up to search Mycobacterium tuberculosis H37Rv (2,118 sequences) database. The following parameters were considered for the searches: peptide mass tolerance was set to 20 ppm, fragment mass tolerance was set to 0.05 Da, and a maximum of two missed cleavage of trypsin was chosen. Carbamidomethyl (C) was set as fixed modification, and oxidation (M), were set as variable modifications. For modification of AEBSF（4-(2-aminoethyl)benzenesulfonyl fluoride hydrochlorideanalysis）,+183.0354 Da was set as a variable modification on serine."],"omics_type":["Proteomics"],"labhead":["Sheng-ce Tao"],"instrument_platform":[""],"submission_type":["COMPLETE"],"labhead_affiliation":["Shanghai Center for Systems Biomedicine  Shanghai Jiao Tong University"],"species":["Escherichia Coli"],"publication":["29622495 Jiang HW, Czajkowsky DM, Wang T, Wang XD, Wang JB, Zhang HN, Liu CX, Wu FL, He X, Xu ZW, Chen H, Guo SJ, Li Y, Bi LJ, Deng JY, Xie J, Pei JF, Zhang XE, Tao SC. Identification of Serine 119 as an Effective Inhibitor Binding Site of M. tuberculosis Ubiquitin-like Protein Ligase PafA Using Purified Proteins and M. smegmatis. EBioMedicine. 2018 30:225-236 10.1016/j.ebiom.2018.03.025"],"submitter_mail":["jhw622@163.com"],"curator_keywords":["Biological"],"submitter_affiliation":["shanghai jiaotong university"],"submitter_country":["China"],"doi":["10.6019/PXD006930"],"pubmed_abstract":["Owing to the spread of multidrug resistance (MDR) and extensive drug resistance (XDR), there is a pressing need to identify potential targets for the development of more-effective anti-M. tuberculosis (Mtb) drugs. PafA, as the sole Prokaryotic Ubiquitin-like Protein ligase in the Pup-proteasome System (PPS) of Mtb, is an attractive drug target. Here, we show that the activity of purified Mtb PafA is significantly inhibited upon the association of AEBSF (4-(2-aminoethyl) benzenesulfonyl fluoride) to PafA residue Serine 119 (S119). Mutation of S119 to amino acids that resemble AEBSF has similar inhibitory effects on the activity of purified Mtb PafA. Structural analysis reveals that although S119 is distant from the PafA catalytic site, it is located at a critical position in the groove where PafA binds the C-terminal region of Pup. Phenotypic studies demonstrate that S119 plays critical roles in the function of Mtb PafA when tested in M. smegmatis. Our study suggests that targeting S119 is a promising direction for developing an inhibitor of M. tuberculosis PafA."],"pubmed_title":["Identification of Serine 119 as an Effective Inhibitor Binding Site of M. tuberculosis Ubiquitin-like Protein Ligase PafA Using Purified Proteins and M. smegmatis."],"pubmed_authors":["Jiang He-Wei HW, Czajkowsky Daniel M DM, Wang Tao T, Wang Xu-De XD, Wang Jia-Bin JB, Zhang Hai-Nan HN, Liu Cheng-Xi CX, Wu Fan-Lin FL, He Xiang X, Xu Zhao-Wei ZW, Chen Hong H, Guo Shu-Juan SJ, Li Yang Y, Bi Li-Jun LJ, Deng Jiao-Yu JY, Xie Jin J, Pei Jian-Feng JF, Zhang Xian-En XE, Tao Sheng-Ce SC"],"description_synonyms":["Site, Binding, liquid chromatography tandem mass spectroscopy, LC-MS2, Combining Site, LC/MS/MS, LCMSMS, determination, liquid chromatography-tandem mass spectroscopy, LC-MSMS, Sites, LC-MS/MS, site, liquid chromatography tandem mass spectrometry, chemical analysis., Combining, assay, Binding Site, Combining Sites, LC-MS-MS"],"data_synonyms":["Bru, IPP2A2, Clo, Raw, AW549739, Slf, SLF, Mycobacterium tuberculosis str. H37Rv, Somatomedin-C, cleavage, FBN, FPH2, thomson, contrasted, PHAPII, mass-to-charge ratio, protrusion, 2-Amino-3-hydroxypropionic acid, 5730420M11Rik, peptide, Polypeptides, Drug Tolerance, peptido, ECTOL1, Del(8)44H, Analysis, WMS, C79691, Svc, SET, peptides, Analyses, TAF-I, ipp2a2, beta-Trypsin, L-Serine., SF, Fluoride, 2pp2a, Kitl, Sciences, Mast cell growth factor, CG10574, OCTD, DmelCG4299, Lccp, mKIAA0989, IGAAD, set, Con, data processing, 2PP2A, 10^[-6], 2-amino-3-hydroxypropanoic acid, DmelCG10574, taf-ibeta, ppm, Mechano growth factor, dSET, dSet, blz, peptidos, Soluble KIT ligand, GPHYSD2, Sl, z, drug tolerance, SGS, phapii, IGF-I, anatomical protrusion, immune system tolerance, igaad, StF-IT-1, Th, IBP1, Mycobacterium sp. H37Rv, Peptide, sKITLG, group, ACMICD, polypeptide, Serin, Immune Tolerance, 3-Hydroxyalanine, I-2PP2A, Algorithm, Dm I-2, I2PP2A, Immunologic Tolerance, MFS1, Igf-1, WMS2, Data Base, SHEP7, Mycobacterium tuberculosis strain H37Rv, Col4a-1, PRSS, HLA-DR-associated protein II, mast cell growth factor, ensemble, DI-2, I-2Dm, Mycobacterium tuberculosis H37Rv, Stem cell factor, Tripcellim, MASCOT, MASS, CG4299, STAT5, beta Trypsin, I-2PP1, Trypure, data analysis, dSET/TAF-Ibeta, Kitlg, 2610030F17Rik, KL-1, TAF-IBETA, Self Tolerance, Tolerance, Data, spine, MGF, Mgf, SSKS, c-Kit ligand, Peptid, L Serine, TAF-Ibeta, Polypeptide, SCF, variable, AA407739, i2pp2a, Gb, Data Analyses, Immunological Tolerance"],"pubmed_title_synonyms":["inhibitors, Kochs Disease, protein complex, Proteins, inhibitor, Gene, Synthetases, ATP Dependent Proteolysis Factor 1, protein, Binding Site, Ubiquitin carboxyl extension protein 80, protein-containing complex, CEP52, 2-Amino-3-hydroxypropionic acid, Binding, Human, Serin, Ubiquitin A-52 residue ribosomal protein fusion product 1, native protein, 3-Hydroxyalanine, Ubiquitin-related 2, Protein, Sites, Infection, Gene Products, Synthetase, Tuberculosis, HMG-20, Tuberculoses, ATP-Dependent Proteolysis Factor 1, protein aggregate, Ubiq, antagonists, Site, Koch's Disease, Ubiquitin, covalent modifier, Koch Disease, High Mobility Protein 20, Infections, Protein., Human Ubiquitin, inhibiteur, Combining, Ubiquitin-related 1, Mycobacterium tuberculosis Infections, Protein Gene Products, Ligase, APF-1, Gene Proteins, Combining Site, 40S ribosomal protein S27a, inhibidor, 2-amino-3-hydroxypropanoic acid, antagonists and inhibitors, 60S ribosomal protein L40, ligase, ubiquitin, site, L Serine, Ubiquitin-related, Mycobacterium tuberculosis, Mycobacterium tuberculosis Infection, L-Serine, Combining Sites, protein tagging activity, active tuberculosis"],"sample_synonyms":["sodium salt, liquid chromatography tandem mass spectroscopy, F10B6_15, ammonium formate, 13C-labeled, MeCN, cadmium salt, nickel formate dihydrate, NCMe, lead formate, determination, Histological Labelings, aluminum salt, cesium salt, zinc formate, Gene, lead salt, SDH, protein, magnesium formate, protein-containing complex, zinc salt, F10B6.15, CG7826, LC-MS-MS, Buffer, formic acid, SDS, Polypeptides, potassium salt, ammonium tetraformate, peptido, reduced, cobalt(II) formate dihydrate, congenital, 14C-labeled, CH3-C#N, LC-MSMS, Gene Products, CG7835, CG42273, Histological, Min, tiny, protein aggregate, DmelCG42273, Pro-Mega, LCMSMS, Staining, peptides, thallium (+1) salt, beta-Trypsin, rubidium salt, hypoplasia, min, chemical analysis., 4733401P19Rik, mAPC, copper, calcium formate, methanoic acid, lipomatosis of pancreas, Solution, AI047805, lithium salt, SOLO DANCERS, congenital lipomatosis of pancreas, peptidos, Shwachman-Bodian syndrome, cromium (+3) salt, ammonium (2:1) salt, sodium formate, Histological Labeling, nickel salt, small, LC-MS2, DYRK1, 1-(14)C-labeled, nickel formate, 3H-labeled, cobalt (+2) salt, protein complex, Proteins, LC-MS/MS, Dmel_CG7826, AI836084, strontium formate, Labeling and Staining, Stainings, potassium formate, Mischung, copper (+2) salt, acetonitrile, strontium salt, buffer, Labeling, Peptide, LC/MS/MS, sodium (4:1:1) salt, native protein, Temperatures, Dm1, magnesium salt, cupric formate, Protein, Dyrk1, aluminum formate, nickel (+2) salt, ACETONITRILE, Dmel_CG7835, cyanomethane, Mnb, MNB, pupylation, AU020952, Pup-protein conjugation, ammonium salt, lithium formate, PRSS, underdeveloped, CC1, formate, Shwachman-Diamond type metaphyseal dysplasia, Tripcellim, cobaltous formate, SWDS, Shwachman-Bodian-Diamond syndrome, cromium (+3), Shwachman syndrome, ethanenitrile, CGI-97, AW124434, beta Trypsin, chromic formate, ME-IV, Protein Gene Products, Gene Proteins, Trypure, Labelings, Pancreatic insufficiency and bone marrow dysfunction, liquid chromatography-tandem mass spectroscopy, copper salt, ammonium (4:1) salt, calcium salt, liquid chromatography tandem mass spectrometry, Peptid, Polypeptide, assay, methyl cyanide, lead (+2) salt"],"pubmed_abstract_synonyms":["retinol (vitamin A1) dehydrogenase activity, single-organism developmental process, Product, Activity, determination, popliteal pterygium syndrome, postnatal development, Aminosaeure, Abcb1, Amino acid, growth and development, protein, PPS1, 2-Amino-3-hydroxypropionic acid, Mutations, Multicatalytic Endopeptidase Complex, Associations, concavities, Pharmaceutical Product, PpS, Tuberculosis, CAPG2, protein aggregate, drug resistance, C62, retinal reductase activity, Koch's Disease, Koch Disease, amino acids, High Mobility Protein 20, facio-genito-popliteal syndrome, Macropain, 5830426I05Rik, OFC6, retinol:NAD+ oxidoreductase activity, PPS, Pps, Fluoride, Ubiquitin-related 1, posterior pharyngeal sensilla, Proteasome Endopeptidase, 20S Proteasome, Ligase, APF-1, geographical area, hpo, 2-amino-3-hydroxypropanoic acid, medicine, Pharmaceutical, cleft lip/palate paramedian mucous cysts of the lower lip popliteal pterygium digital and genital anomalies, 26S proteasome, remote from, all-trans retinol dehydrogenase activity, Organ X, Proteinase, Endopeptidase Complex, Aminokarbonsaeure, VWS1, CEP52, alpha-amino carboxylic acids, Ingensin, larval pharyngeal sense organ, 3-Hydroxyalanine, fossae, Pharmaceutic, digital and genital anomalies, hCAP-G2, region, Ubiq, Mycobacterium tuberculosis., Ubiquitin, proteasome, Amino Acid, Acid, positional polypeptide feature, Amino acids, CAP-G2, general secretion pathway-associated complex, Human Ubiquitin, popliteal pterygium, depressions, antagonists and inhibitors, Pgy-1, L Serine, Acids, Mycobacterium tuberculosis Infection, L-Serine, active tuberculosis, Pgy1, region or site annotation, drug susceptibility/resistance, Luzp5, Aminocarbonsaeure, Gene, Synthetases, ATP Dependent Proteolysis Factor 1, Ubiquitin carboxyl extension protein 80, alpha-amino acid, protein-containing complex, Human, Sec-dependent secretion system-associated complex, Multicatalytic Proteinase, resistance, Gene Products, HMG-20, cleft Lip/palate, Mdr1b, Drugs, study, positional, DmelCG6525, anatomical systems, Infections, retinene reductase activity, Direction, LPS, Complex, inhibiteur, Mycobacterium tuberculosis Infections, SKIP, FBgn0082831, concavity, 40S ribosomal protein S27a, drugs, mCAP-G2, Multicatalytic Endopeptidase, inhibidor, Multicatalytic, ubiquitin, Macroxyproteinase, main terminal branch, site, Mycobacterium tuberculosis, Preparation, protein tagging activity, MTB, Mtb, PIT, Pharmaceuticals, microsomal retinol dehydrogenase activity, paramedian mucous cysts of the Lower Lip, inhibitors, Products, Kochs Disease, Drug resistance, protein complex, drug, Proteins, Spp, SPP, inhibitor, alpha-amino acids, function, Medications, MDR, Proteasome, development, T2SS-associated complexes, Serin, Ubiquitin A-52 residue ribosomal protein fusion product 1, native protein, Ubiquitin-related 2, Protein, chemical analysis, Resistance, Infection, Synthetase, sequence, spp, VWS, Tuberculoses, ATP-Dependent Proteolysis Factor 1, mdr, cell surface groove, distant from, LUZP5, antagonists, covalent modifier, groove, Pharmaceutic Preparations, Prosome, response to drug, postnatal growth, Mdr1, 20S, faciogenitopopliteal syndrome, Amino, primary structure of sequence macromolecule, Polio and Post-Polio Syndrome, Drug, Protein Gene Products, Gene Proteins, Preparations, 60S ribosomal protein L40, ligase, CG6525, Ubiquitin-related, assay, X-organ of Keilin, Pharmaceutical Products, multicatalytic endopeptidase, growth, General activity, depression, Pharmaceutical Preparation, proteasome endopeptidase complex"],"name_synonyms":["2-Amino-3-hydroxypropionic acid, antagonists, Site, Binding, inhibitors, Combining Site, Serin, inhibidor, 2-amino-3-hydroxypropanoic acid, 3-Hydroxyalanine, antagonists and inhibitors, Binding., Sites, site, L Serine, inhibiteur, inhibitor, Combining, Binding Site, L-Serine, Combining Sites"],"additional_accession":[]},"is_claimable":false,"name":"PafA-ABESF -  Identification of Serine 119 as an Effective Inhibitor Binding Site of M","description":"Identified AEBSF binding site of PafA by LC-MS/MS 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