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Hemu X, El Sahili A, Hu S, Zhang X, Serra A, Goh BC, Darwis DA, Chen MW, Sze SK, Liu CF, Lescar J, Tam JP. Turning an Asparaginyl Endopeptidase into a Peptide Ligase. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02078] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Xinya Hemu
- Synzymes and Natural Products Center (SYNC), School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Abbas El Sahili
- Synzymes and Natural Products Center (SYNC), School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
- NTU Institute of Structural Biology, Nanyang Technological University, Experimental Medicine Building, 59 Nanyang Drive, Singapore 636921
| | - Side Hu
- Synzymes and Natural Products Center (SYNC), School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
- NTU Institute of Structural Biology, Nanyang Technological University, Experimental Medicine Building, 59 Nanyang Drive, Singapore 636921
| | - Xiaohong Zhang
- Synzymes and Natural Products Center (SYNC), School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Aida Serra
- Synzymes and Natural Products Center (SYNC), School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
- IMDEA Food Research Institute, Carr. de Canto Blanco, 8, Madrid 28049, Spain
| | - Boon Chong Goh
- NTU Institute of Structural Biology, Nanyang Technological University, Experimental Medicine Building, 59 Nanyang Drive, Singapore 636921
- Antimicrobial Resistance Interdisciplinary Research Group, SMART, 1 CREATE Way, Singapore 138602
| | - Dina A. Darwis
- Synzymes and Natural Products Center (SYNC), School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
- Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, 14 Medical Drive, Singapore 117599
| | - Ming Wei Chen
- Synzymes and Natural Products Center (SYNC), School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Siu Kwan Sze
- Synzymes and Natural Products Center (SYNC), School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Chuan-fa Liu
- Synzymes and Natural Products Center (SYNC), School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Julien Lescar
- Synzymes and Natural Products Center (SYNC), School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
- NTU Institute of Structural Biology, Nanyang Technological University, Experimental Medicine Building, 59 Nanyang Drive, Singapore 636921
| | - James P. Tam
- Synzymes and Natural Products Center (SYNC), School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
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Khavrutskii IV, Compton JR, Jurkouich KM, Legler PM. Paired Carboxylic Acids in Enzymes and Their Role in Selective Substrate Binding, Catalysis, and Unusually Shifted p Ka Values. Biochemistry 2019; 58:5351-5365. [PMID: 31192586 DOI: 10.1021/acs.biochem.9b00429] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cathepsin A (CatA, EC 3.4.16.5, UniProtKB P10619 ) is a human lysosomal carboxypeptidase. Counterintuitively, crystal structures of CatA and its homologues show a cluster of Glu and Asp residues binding the C-terminal carboxylic acid of the product or inhibitor. Each of these enzymes functions in an acidic environment and contains a highly conserved pair of Glu residues with side chain carboxyl group oxygens that are approximately 2.3-2.6 Å apart. In small molecules, carboxyl groups separated by ∼3 Å can overcome the repulsive interaction by protonation of one of the two groups. The pKa of one group increases (pKa ∼ 11) and can be as much as ∼6 pH units higher than the paired group. Consequently, at low and neutral pH, one carboxylate can carry a net negative charge while the other can remain protonated and neutral. In CatA, E69 and E149 form a Glu pair that is important to catalysis as evidenced by the 56-fold decrease in kcat/Km in the E69Q/E149Q variant. Here, we have measured the pH dependencies of log(kcat), log(Km), and log(kcat/Km) for wild type CatA and its variants and have compared the measured pKa with calculated values. We propose a substrate-assisted mechanism in which the high pKa of E149 (>8.5) favors the binding of the carboxylate form of the substrate and promotes the abstraction of the proton from H429 of the catalytic triad effectively decreasing its pKa in a low-pH environment. We also identify a similar motif consisting of a pair of histidines in S-formylglutathione hydrolase.
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Affiliation(s)
- Ilja V Khavrutskii
- Armed Forces Radiobiology Research Institute , Uniformed Services University , Bethesda , Maryland 20889-5648 , United States
| | - Jaimee R Compton
- U.S. Naval Research Laboratory , 4555 Overlook Avenue , Washington, D.C. 20375 , United States
| | - Kayla M Jurkouich
- Department of Biomedical Engineering , Case Western Reserve University , Cleveland , Ohio 44106 , United States
| | - Patricia M Legler
- U.S. Naval Research Laboratory , 4555 Overlook Avenue , Washington, D.C. 20375 , United States
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Stennicke HR, Mortensen UH, Breddam K. Studies on the hydrolytic properties of (serine) carboxypeptidase Y. Biochemistry 1996; 35:7131-41. [PMID: 8679540 DOI: 10.1021/bi952758e] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The activity of serine carboxypeptidases is dependent on a catalytic triad, an oxyanion hole, and a binding site equivalent to those found in the serine endopeptidases. The action of carboxypeptidase Y on substrates containing amino acids, alcohols, and amines as leaving groups is described. It is demonstrated that the features common to serine endopeptidases and carboxypeptidases are sufficient for hydrolysis of ester bonds. However, rapid hydrolysis of amide bonds is dependent on interactions between the C-terminal carboxylate group of the substrate and the C-terminal recognition site of the enzyme. Furthermore, on the basis of the pH dependencies of wild-type and mutant enzyme, combined with the ability of the enzyme to utilize binding energy to promote catalysis, alternative models for the high activity of carboxypeptidase Y at low pH are discussed. They describe how the catalytically essential histidine is maintained in its active deprotonated state through perturbation of its pKa value in the enzyme-substrate complex.
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Affiliation(s)
- H R Stennicke
- Carlsberg Laboratory, Department of Chemistry, Copenhagen, Denmark
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Jung G, Ueno H, Hayashi R, Liao TH. Identification of the catalytic histidine residue participating in the charge-relay system of carboxypeptidase Y. Protein Sci 1995; 4:2433-5. [PMID: 8563642 PMCID: PMC2143012 DOI: 10.1002/pro.5560041123] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The essential histidine residue of carboxypeptidase Y (CPY) was modified by a site-specific reagent, a chloromethylketone derivative of benzyloxycarbonyl-L-phenylalanine. The single modified histidine residue was converted to N tau-carboxy-methyl histidine (cmHis) upon performic acid oxidation. A peptide containing cmHis was isolated from the tryptic-thermolytic digest. Based on the amino acid composition and sequence analysis, the peptide is shown to be Val-Phe-Asp-Gly-Gly-cmHis-MetO2-Val-Pro, which was derived from CPY cleaved by trypsin at Arg 391 and thermolysin at Phe 401, and thus His 397 was modified. This histidine residue has been implicated previously by X-ray analysis to participate in the charge-relay system of CPY.
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Affiliation(s)
- G Jung
- Department of Agricultural Chemistry, Faculty of Agriculture, Kyoto University, Japan
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Chiba Y, Midorikawa T, Ichishima E. Cloning and expression of the carboxypeptidase gene from Aspergillus saitoi and determination of the catalytic residues by site-directed mutagenesis. Biochem J 1995; 308 ( Pt 2):405-9. [PMID: 7772020 PMCID: PMC1136940 DOI: 10.1042/bj3080405] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Carboxypeptidase from Aspergillus saitoi removes acidic, neutral and basic amino acids as well as proline from the C-terminal position at pH 2-5. cpdS, a cDNA encoding A. saitoi carboxypeptidase, was cloned and expressed. Analysis of the 1816-nucleotide sequence revealed a single open reading frame coding for 523 amino acids. When A. saitoi carboxypeptidase cDNA was expressed in yeast cells, carboxypeptidase activity was detected in the cell extract and was immunostained with a 72 kDa protein with polyclonal anti-(A. saitoi carboxypeptidase) serum. The recombinant enzyme treated with glycopeptidase F migrated with an apparent molecular mass of 60 kDa on SDS/PAGE, which was the same as that of the de-N-glycosylated carboxypeptidase from A. saitoi. Site-directed mutagenesis of the cpdS indicated that Ser-153, Asp-357 and His-436 residues were essential for the enzymic catalysis. It can be concluded that A. saitoi carboxypeptidase has a catalytic triad comprising Asp-His-Ser and is a member of serine carboxypeptidase family (EC 3.4.16.1).
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Affiliation(s)
- Y Chiba
- Department of Applied Biological Chemistry, Faculty of Agriculture, Tohoku University, Sendai, Japan
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