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Ozhelvaci F, Steczkiewicz K. Identification and Classification of Papain-like Cysteine Proteinases. J Biol Chem 2023:104801. [PMID: 37164157 DOI: 10.1016/j.jbc.2023.104801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 04/11/2023] [Accepted: 05/05/2023] [Indexed: 05/12/2023] Open
Abstract
Papain-like cysteine peptidases form a big and highly diverse superfamily of proteins involved in many important biological functions, such as protein turnover, deubiquitination, tissue remodeling, blood clotting, virulence, defense, and cell wall remodeling. High sequence and structure diversity observed within these proteins hinders their comprehensive classification as well as the identification of new representatives. Moreover, in general protein databases, many families already classified as papain-like lack details regarding their mechanism of action or biological function. Here, we use transitive remote homology searches and 3D modeling to newly classify 21 families to the papain-like cysteine peptidase superfamily. We attempt to predict their biological function, and provide structural chacterization of 89 protein clusters defined based on sequence similarity altogether spanning 106 papain-like families. Moreover, we systematically discuss observed diversity in sequences, structures, and catalytic sites. Eventually, we expand the list of human papain-related proteins by seven representatives, including dopamine receptor-interacting protein (DRIP1) as potential deubiquitinase, and centriole duplication regulating CEP76 as retaining catalytically active peptidase-like domain. The presented results not only provide structure-based rationales to already existing peptidase databases but also may inspire further experimental research focused on peptidase-related biological processes.
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Affiliation(s)
- Fatih Ozhelvaci
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Kamil Steczkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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2
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Zhao JY, Yuan XK, Luo RZ, Wang LX, Gu W, Yamane D, Feng H. Phospholipase A and acyltransferase 4/retinoic acid receptor responder 3 at the intersection of tumor suppression and pathogen restriction. Front Immunol 2023; 14:1107239. [PMID: 37063830 PMCID: PMC10102619 DOI: 10.3389/fimmu.2023.1107239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 03/22/2023] [Indexed: 04/03/2023] Open
Abstract
Phospholipase A and acyltransferase (PLAAT) 4 is a class II tumor suppressor with phospholipid metabolizing abilities. It was characterized in late 2000s, and has since been referred to as ‘tazarotene-induced gene 3’ (TIG3) or ‘retinoic acid receptor responder 3’ (RARRES3) as a key downstream effector of retinoic acid signaling. Two decades of research have revealed the complexity of its function and regulatory roles in suppressing tumorigenesis. However, more recent findings have also identified PLAAT4 as a key anti-microbial effector enzyme acting downstream of interferon regulatory factor 1 (IRF1) and interferons (IFNs), favoring protection from virus and parasite infections. Unveiling the molecular mechanisms underlying its action may thus open new therapeutic avenues for the treatment of both cancer and infectious diseases. Herein, we aim to summarize a brief history of PLAAT4 discovery, its transcriptional regulation, and the potential mechanisms in tumor prevention and anti-pathogen defense, and discuss potential future directions of PLAAT4 research toward the development of therapeutic approaches targeting this enzyme with pleiotropic functions.
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Affiliation(s)
- Jian-Yong Zhao
- Hospital of Integrated Traditional Chinese and Western Medicine, Hebei University of Chinese Medicine, Cangzhou, Hebei, China
| | - Xiang-Kun Yuan
- Hospital of Integrated Traditional Chinese and Western Medicine, Hebei University of Chinese Medicine, Cangzhou, Hebei, China
| | - Rui-Zhen Luo
- Hospital of Integrated Traditional Chinese and Western Medicine, Hebei University of Chinese Medicine, Cangzhou, Hebei, China
| | - Li-Xin Wang
- Hospital of Integrated Traditional Chinese and Western Medicine, Hebei University of Chinese Medicine, Cangzhou, Hebei, China
| | - Wei Gu
- School of Medicine, Chongqing University, Chongqing, China
| | - Daisuke Yamane
- Department of Diseases and Infection, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
- *Correspondence: Hui Feng, ; Daisuke Yamane,
| | - Hui Feng
- School of Medicine, Chongqing University, Chongqing, China
- *Correspondence: Hui Feng, ; Daisuke Yamane,
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3
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Chatterjee SD, Zhou J, Dasgupta R, Cramer-Blok A, Timmer M, van der Stelt M, Ubbink M. Protein Dynamics Influence the Enzymatic Activity of Phospholipase A/Acyltransferases 3 and 4. Biochemistry 2021; 60:1178-1190. [PMID: 33749246 PMCID: PMC8154263 DOI: 10.1021/acs.biochem.0c00974] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Phospholipase A/acyltransferase
3 (PLAAT3) and PLAAT4 are enzymes
involved in the synthesis of bioactive lipids. Despite sequential
and structural similarities, the two enzymes differ in activity and
specificity. The relation between the activity and dynamics of the
N-terminal domains of PLAAT3 and PLAAT4 was studied. PLAAT3 has a
much higher melting temperature and exhibits less nanosecond and millisecond
dynamics in the active site, in particular in loop L2(B6), as shown
by NMR spectroscopy and molecular dynamics calculations. Swapping
the L2(B6) loops between the two PLAAT enzymes results in strongly
increased phospholipase activity in PLAAT3 but no reduction in PLAAT4
activity, indicating that this loop contributes to the low activity
of PLAAT3. The results show that, despite structural similarity, protein
dynamics differ substantially between the PLAAT variants, which can
help to explain the activity and specificity differences.
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Affiliation(s)
- Soumya Deep Chatterjee
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Juan Zhou
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Rubin Dasgupta
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Anneloes Cramer-Blok
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Monika Timmer
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Mario van der Stelt
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Marcellus Ubbink
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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4
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Lipoprotein N-Acylation in Staphylococcus aureus Is Catalyzed by a Two-Component Acyl Transferase System. mBio 2020; 11:mBio.01619-20. [PMID: 32723923 PMCID: PMC7387801 DOI: 10.1128/mbio.01619-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Although it has long been known that S. aureus forms triacylated Lpps, a lack of homologs to known N-acylation genes found in Gram-negative bacteria has until now precluded identification of the genes responsible for this Lpp modification. Here, we demonstrate N-terminal Lpp acylation and chemotype conversion to the tri-acylated state is directed by a unique acyl transferase system encoded by two noncontiguous staphylococci genes (lnsAB). Since triacylated Lpps stimulate TLR2 more weakly than their diacylated counterparts, Lpp N-acylation is an important TLR2 immunoevasion factor for determining tolerance or nontolerance in niches such as in the skin microbiota. The discovery of the LnsAB system expands the known diversity of Lpp biosynthesis pathways and acyl transfer biochemistry in bacteria, advances our understanding of Lpp structural heterogeneity, and helps differentiate commensal and noncommensal microbiota. Bacterial lipoproteins (Lpps) are a class of membrane-associated proteins universally distributed among all bacteria. A characteristic N-terminal cysteine residue that is variably acylated anchors C-terminal globular domains to the extracellular surface, where they serve numerous roles, including in the capture and transport of essential nutrients. Lpps are also ligands for the Toll-like receptor 2 (TLR2) family, a key component of the innate immune system tasked with bacterial recognition. While Lpp function is conserved in all prokaryotes, structural heterogeneity in the N-terminal acylation state is widespread among Firmicutes and can differ between otherwise closely related species. In this study, we identify a novel two-gene system that directs the synthesis of N-acylated Lpps in the commensal and opportunistic pathogen subset of staphylococci. The two genes, which we have named the lipoprotein N-acylation transferase system (Lns), bear no resemblance to previously characterized N-terminal Lpp tailoring enzymes. LnsA (SAOUHSC_00822) is an NlpC/P60 superfamily enzyme, whereas LnsB (SAOHSC_02761) has remote homology to the CAAX protease and bacteriocin-processing enzyme (CPBP) family. Both LnsA and LnsB are together necessary and alone sufficient for N-acylation in Staphylococcus aureus and convert the Lpp chemotype from diacyl to triacyl when heterologously expressed in Listeria monocytogenes. Acquisition of lnsAB decreases TLR2-mediated detection of S. aureus by nearly 10-fold and shifts the activated TLR2 complex from TLR2/6 to TLR2/1. LnsAB thus has a dual role in attenuating TLR2 signaling in addition to a broader role in bacterial cell envelope physiology.
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5
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Zhou J, Mock ED, Martella A, Kantae V, Di X, Burggraaff L, Baggelaar MP, Al-Ayed K, Bakker A, Florea BI, Grimm SH, den Dulk H, Li CT, Mulder L, Overkleeft HS, Hankemeier T, van Westen GJP, van der Stelt M. Activity-Based Protein Profiling Identifies α-Ketoamides as Inhibitors for Phospholipase A2 Group XVI. ACS Chem Biol 2019; 14:164-169. [PMID: 30620559 PMCID: PMC6379856 DOI: 10.1021/acschembio.8b00969] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/08/2019] [Indexed: 02/07/2023]
Abstract
Phospholipase A2, group XVI (PLA2G16) is a thiol hydrolase from the HRASLS family that regulates lipolysis in adipose tissue and has been identified as a host factor enabling the cellular entry of picornaviruses. Chemical tools are essential to visualize and control PLA2G16 activity, but they have not been reported to date. Here, we show that MB064, which is a fluorescent lipase probe, also labels recombinant and endogenously expressed PLA2G16. Competitive activity-based protein profiling (ABPP) using MB064 enabled the discovery of α-ketoamides as the first selective PLA2G16 inhibitors. LEI110 was identified as a potent PLA2G16 inhibitor ( Ki = 20 nM) that reduces cellular arachidonic acid levels and oleic acid-induced lipolysis in human HepG2 cells. Gel-based ABPP and chemical proteomics showed that LEI110 is a selective pan-inhibitor of the HRASLS family of thiol hydrolases (i.e., PLA2G16, HRASLS2, RARRES3 and iNAT). Molecular dynamic simulations of LEI110 in the reported crystal structure of PLA2G16 provided insight in the potential ligand-protein interactions to explain its binding mode. In conclusion, we have developed the first selective inhibitor that can be used to study the cellular role of PLA2G16.
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Affiliation(s)
- Juan Zhou
- Department
of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Elliot D. Mock
- Department
of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Andrea Martella
- Department
of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Vasudev Kantae
- Department
of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
- Department
of Analytical BioSciences and Metabolomics, Leiden Academic Centre
for Drug Research, Leiden University, Leiden, The Netherlands
| | - Xinyu Di
- Department
of Analytical BioSciences and Metabolomics, Leiden Academic Centre
for Drug Research, Leiden University, Leiden, The Netherlands
| | - Lindsey Burggraaff
- Department
of Computational Drug Discovery, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Marc P. Baggelaar
- Department
of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Karol Al-Ayed
- Department
of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Alexander Bakker
- Department
of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Bogdan I. Florea
- Department
of Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Sebastian H. Grimm
- Department
of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Hans den Dulk
- Department
of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Chun T. Li
- Department
of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Laura Mulder
- Department
of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Herman S. Overkleeft
- Department
of Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Thomas Hankemeier
- Department
of Analytical BioSciences and Metabolomics, Leiden Academic Centre
for Drug Research, Leiden University, Leiden, The Netherlands
| | - Gerard J. P. van Westen
- Department
of Computational Drug Discovery, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Mario van der Stelt
- Department
of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
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6
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Wei H, Wang L, Ren X, Yu W, Lin J, Jin C, Xia B. Structural and functional characterization of tumor suppressors TIG3 and H-REV107. FEBS Lett 2015; 589:1179-86. [PMID: 25871522 DOI: 10.1016/j.febslet.2015.04.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 03/16/2015] [Accepted: 04/01/2015] [Indexed: 11/30/2022]
Abstract
H-REV107-like family proteins TIG3 and H-REV107 are class II tumor suppressors. Here we report that the C-terminal domains (CTDs) of TIG3 and H-REV107 can induce HeLa cell death independently. The N-terminal domain (NTD) of TIG3 enhances the cell death inducing ability of CTD, while NTD of H-REV107 plays an inhibitory role. The solution structure of TIG3 NTD is very similar to that of H-REV107 in overall fold. However, the CTD binding regions on NTD are different between TIG3 and H-REV107, which may explain their functional difference. As a result, the flexible main loop of H-REV107, but not that of TIG3, is critical for its NTD to modulate its CTD in inducing cell death.
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Affiliation(s)
- Hejia Wei
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China; School of Life Sciences, Peking University, Beijing 100871, China
| | - Lei Wang
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China; College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiaobai Ren
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China; College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wenyu Yu
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China; School of Life Sciences, Peking University, Beijing 100871, China
| | - Jian Lin
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China; College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Changwen Jin
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China; School of Life Sciences, Peking University, Beijing 100871, China; College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Bin Xia
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China; School of Life Sciences, Peking University, Beijing 100871, China; College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
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