Holger A. Lindner

The Papain-Like Protease from the Severe Acute Respiratory Syndrome Coronavirus Is a Deubiquitinating Enzyme

ABSTRACT The severe acute respiratory syndrome coronavirus papain-like protease (SARS-CoV PLpro) is involved in the processing of the viral polyprotein and, thereby, contributes to the biogenesis of the virus replication complex. Structural bioinformatics has revealed a relationship for the SARS-CoV PLpro to herpesvirus-associated ubiquitin-specific protease (HAUSP), a ubiquitin-specific protease, indicating potential deubiquitinating activity in addition to its function in polyprotein processing (T. Sulea, H. A. Lindner, E. O. Purisima, and R. Menard, J. Virol. 79:4550-4551, 2005). In order to confirm this prediction, we overexpressed and purified SARS-CoV PLpro (amino acids [aa]1507 to 1858) from Escherichia coli. The purified enzyme hydrolyzed ubiquitin-7-amino-4-methylcoumarin (Ub-AMC), a general deubiquitinating enzyme substrate, with a catalytic efficiency of 13,100 M−1s−1, 220-fold more efficiently than the small synthetic peptide substrate Z-LRGG-AMC, which incorporates the C-terminal four residues of ubiquitin. In addition, SARS-CoV PLpro was inhibited by the specific deubiquitinating enzyme inhibitor ubiquitin aldehyde, with an inhibition constant of 210 nM. The purified SARS-CoV PLpro disassembles branched polyubiquitin chains with lengths of two to seven (Ub2-7) or four (Ub4) units, which involves isopeptide bond cleavage. SARS-CoV PLpro processing activity was also detected against a protein fused to the C terminus of the ubiquitin-like modifier ISG15, both in vitro using the purified enzyme and in HeLa cells by coexpression with SARS-CoV PLpro (aa 1198 to 2009). These results clearly establish that SARS-CoV PLpro is a deubiquitinating enzyme, thereby confirming our earlier prediction. This unexpected activity for a coronavirus papain-like protease suggests a novel viral strategy to modulate the host cell ubiquitination machinery to its advantage.

Selectivity in ISG15 and ubiquitin recognition by the SARS coronavirus papain-like protease

Abstract The severe acute respiratory syndrome coronavirus papain-like protease (SARS-CoV PLpro) carries out N-terminal processing of the viral replicase polyprotein, and also exhibits Lys48-linked polyubiquitin chain debranching and ISG15 precursor processing activities in vitro. Here, we used SDS–PAGE and fluorescence-based assays to demonstrate that ISG15 derivatives are the preferred substrates for the deubiquitinating activity of the PLpro. With k cat/K M of 602,000M−1 s−1, PLpro hydrolyzes ISG15-AMC 30- and 60-fold more efficiently than Ub-AMC and Nedd8-AMC, respectively. Data obtained with truncated ISG15 and hybrid Ub/ISG15 substrates indicate that both the N- and C-terminal Ub-like domains of ISG15 contribute to this preference. The enzyme also displays a preference for debranching Lys48- over Lys63-linked polyubiquitin chains. Our results demonstrate that SARS-CoV PLpro can differentiate between ubiquitin-like modifiers sharing a common C-terminal sequence, and that the debranching activity of the PLpro is linkage type selective. The potential structural basis for the demonstrated specificity of SARS-CoV PLpro is discussed.

Essential roles of zinc ligation and enzyme dimerization for catalysis in the aminoacylase-1/M20 family

Members of the aminoacylase-1 (Acy1)/M20 family of aminoacylases and exopeptidases exist as either monomers or homodimers. They contain a zinc-binding domain and a second domain mediating dimerization in the latter case. The roles that both domains play in catalysis have been investigated for human Acy1 (hAcy1) by x-ray crystallography and by site-directed mutagenesis. Structure comparison of the dinuclear zinc center in a mutant of hAcy1 reported here with dizinc centers in related enzymes points to a difference in zinc ligation in the Acy1/M20 family. Mutational analysis supports catalytic roles of zinc ions, a vicinal glutamate, and a histidine from the dimerization domain. By complementing different active site mutants of hAcy1, we show that catalysis occurs at the dimer interface. Reinterpretation of the structure of a monomeric homolog, peptidase V, reveals that a domain insertion mimics dimerization. We conclude that monomeric and dimeric Acy1/M20 family members share a unique active site architecture involving both enzyme domains. The study may provide means to improve homologous carboxypeptidase G2 toward application in antibody-directed enzyme prodrug therapy.

Deubiquitination, a New Function of the Severe Acute Respiratory Syndrome Coronavirus Papain-Like Protease?

A new coronavirus has been identified as the infectious agent of severe acute respiratory syndrome (SARS). Although SARS was successfully contained by quarantine measures, the reconstructed itinerary of the virus through 30 countries and its high mortality rate illustrate the global threat that this newly emerging disease represents (17). During the expression of the SARS coronavirus (SCoV) genome, two viral cysteine proteases, a papain-like protease (PLpro) and a chymotrypsin-like protease (3CLpro), process the encoded polyprotein precursor to release most of the proteins required for virus replication. PLpro refers to a domain of nonstructural protein 3, whose boundaries are defined by homology to the papain-like fold (7). The PLpro domain can be regarded as the catalytic core behind PLpro-mediated cleavages, even though processing by PLpros has been reported to be modulated by additional amino acid residues outside of these boundaries (15, 18). The SCoV utilizes a single PLpro, whereas most coronaviruses contain two paralogous enzymes, termed PL1pro and PL2pro (14). PLpros in general are not as well characterized as 3CLpros and have not generated as much interest as pharmaceutical targets. However, further structure-to-function annotations might refocus the attention on PLpros. For this purpose, we mined the current Protein Data Bank (PDB) content using the Structure Prediction Meta Server (http://www.bioinfo.pl/meta), which assembles state-of-the-art fold recognition methods and provides a consensus sequence-to-structure hyperscore with the 3D-Jury method (4). The only highly reliable prediction (3D-Jury score > 100) obtained for the SCoV PLpro sequence from K1632 to E1847 was the structure of the catalytic core domain of the herpesvirus-associated ubiquitin-specific protease (HAUSP), also known as USP7 (8). There is compelling evidence for the relevance of a structural relationship between SCoV PLpro and HAUSP (Fig. ​(Fig.1).1). First, HAUSP is a cysteine protease with a finger domain inserted between the two subdomains of a papain-like fold (8). This structure mirrors the general architecture proposed for the members of the coronaviral PLpro family, which now includes SCoV PLpro, with a Zn ribbon domain inserted in the middle of a papain-like protease domain (7). Our structural bioinformatics data support a circularly permuted rather than a classical Zn ribbon domain for SCoV PLpro, as was recently reported for HAUSP and related enzymes (12). Second, as a deubiquitinating enzyme, HAUSP recognizes the C-terminal ubiquitin sequence, LRGG, which matches the narrow specificity profile of SCoV PLpro (LXGG) derived from the three PLpro-processing sites of the polyprotein (6, 16). The modeled SCoV PLpro binding site is highly complementary to the LXGG sequence and establishes extensive hydrogen bonding with the substrate main chain. In particular, significant occlusions of the S1 subsite (due to N1649 and L1702) and S2 subsite (due to Y1804 and Y1813) account for the strict specificity for diglycine at substrate positions P1 and P2 (Fig. ​(Fig.1C).1C). The structural signatures for strict specificity are present in human coronavirus (HCoV 229E) PL1pro and PL2pro as well as in mouse hepatitis virus (MHV) PL2pro but not in MHV PL1pro (Fig. ​(Fig.1D).1D). This fact correlates with the available specificity data showing a preference for the large arginine residue at the P2 position in the case of MHV PL1pro (2, 3, 9) and with the observation that the irreversible inhibitor E-64d, which contains a bulky P2 residue (leucine), inhibits MHV PL1pro (5, 11) but not MHV PL2pro (10). FIG. 1. Structure-to-function relationships between SCoV PLpro and HAUSP. (A) Three-dimensional model of SCoV PLpro. The protease domain is rendered in cyan, and the circularly permuted Zn ribbon domain is shown in red. The zinc ion is shown as a magenta sphere, ... Structural similarities to HAUSP suggest that, in addition to polyprotein processing activity, SCoV PLpro might possess deubiquitinating activity (including deconjugation of other ubiquitin-like modifiers), as was observed for an adenoviral protease (1). This unexpected activity prediction raises provocative hypotheses regarding the ability of the SARS virus to evade cellular defense mechanisms. For example, it is tempting to speculate that ISG15 deconjugation by PLpro allows the SARS virus to counteract protein ISGylation, an interferon-induced process that may contribute to innate immunity to viral infection (13). The deubiquitination function would greatly impact the value of PLpro as a therapeutic target and provide a framework for the development of antivirals to treat SARS. Strategies for the design of inhibitors of SCoV PLpro must also take into consideration the potentially overlapping specificity of this protease with those of cellular deubiquitinating enzymes. Our finding suggests the performance of follow-up experiments that will increase the understanding of the functional roles of papain-like proteases in the viral life cycles of SCoV and related viruses.

Deubiquitination in virus infection.

Abstract Post-translational modification of proteins and peptides by ubiquitin, a highly evolutionarily conserved 76 residue protein, and ubiquitin-like modifiers has emerged as a major regulatory mechanism in various cellular activities. Eukaryotic viruses are known to modulate protein ubiquitination to their advantage in various ways. At the same time, the evidence for the importance of deubiquitination as a viral target also is growing. This review centers on known viral interactions with protein deubiquitination, on viral enzymes for which deubiquitinating activities were recently demonstrated, and on the roles of viral ubiquitin-like sequences.

The distribution of aminoacylase I among mammalian species and localization of the enzyme in porcine kidney.

Aminoacylase I (Acy-1, EC 3.5.1.14) is found in many mammalian tissues, with highest activities occurring in kidney. The enzyme hydrolyzes a variety of N-acylated amino acids; however, the physiological role and the exact cellular localization of Acy-1 are still a matter of debate. The comparison of Acy-1 activities in kidney and liver homogenates of 11 mammalian species showed that the enzyme is most abundant in true herbivores such as sheep and cattle as well as in omnivores, while activities were very low in both rodents and the cat. Acy-1 activity was not detected in livers of dogs of five different breeds. Using in situ hybridization of porcine kidney sections with DIG-labeled RNA probes, Acy-1 mRNA was shown to be evenly distributed throughout the tubular system, while glomeruli and the interstitium were free of stain. During subcellular fractionation, porcine Acy-1 behaved like a typical cytosolic enzyme. Commonly, Acy-1 is thought to catalyze hydrolytic reactions, i.e., the formation of free amino acids from acylated derivatives. Based on the present results and literature data, we propose a novel hypothesis, i.e., that Acy-1 catalyzes the synthesis (rather than the hydrolysis) of hippurate that is formed as a detoxification product of aromatic compounds.

Structural aspects of recently discovered viral deubiquitinating activities.

Abstract Protein ubiquitination has been identified as a regulatory mechanism in key cellular activities, and deubiquitination is recognized as an important step in processes governed by ubiquitin and ubiquitin-like modifiers. Viruses are known to target ubiquitin and ubiquitin-like modifier pathways using various strategies, including the recruitment of host deubiquitinating enzymes. Deubiquitinating activities have recently been described for proteins from three different virus families (adenovirus, coronavirus and herpesvirus), and predicted for others. This review centers on structural-functional aspects that characterize the confirmed viral deubiquitinating enzymes, and their relationships to established families of cellular deubiquitinating enzymes.

N-acetylamino acid utilization by kidney aminoacylase-1

Mammalian aminoacylase-1 (Acy1) participates in the breakdown of N-acetylated amino acids during intracellular protein catabolism. Acy1 is most abundantly expressed in the kidney tubular epithelium. Lately, Acy1 deficiency was identified in children with increased urinary excretion of several N-acetylamino acids. Here we report detailed N-acetylamino acid specificity profiles for human and porcine Acy1 based on steady state kinetic measurements. We found that LLC-PK1 cells, a model of the porcine kidney proximal tubular epithelium, robustly express Acy1. For the first time, we demonstrate uptake and utilization of N-acteylleucine and -methionine in replacement of the free amino acid, respectively, in cultured epithelial cells. Our data are consistent with a specific role of kidney Acy1 in the salvage of amino acids originating from systemic degradation of N-acetylated proteins.

Binding site-based classification of coronaviral papain-like proteases

The coronavirus replicase gene encodes one or two papain‐like proteases (termed PL1pro and PL2pro) implicated in the N‐terminal processing of the replicase polyprotein and thus contributing to the formation of the viral replicase complex that mediates genome replication. Using consensus fold recognition with the 3D‐JURY meta‐predictor followed by model building and refinement, we developed a structural model for the single PLpro present in the severe acute respiratory syndrome coronavirus (SCoV) genome, based on significant structural relationships to the catalytic core domain of HAUSP, a ubiquitin‐specific protease (USP). By combining the SCoV PLpro model with comparative sequence analyses we show that all currently known coronaviral PLpros can be classified into two groups according to their binding site architectures. One group includes all PL2pros and some of the PL1pros, which are characterized by a restricted USP‐like binding site. This group is designated the R‐group. The remaining PL1pros from some of the coronaviruses form the other group, featuring a more open papain‐like binding site, and is referred to as the O‐group. This two‐group, binding site‐based classification is consistent with experimental data accumulated to date for the specificity of PLpro‐mediated polyprotein processing and PLpro inhibition. It also provides an independent evaluation of the similarity‐based annotation of PLpro‐mediated cleavage sites, as well as a basis for comparison with previous groupings based on phylogenetic analyses. Proteins 2006.

Probing the Acyl-Binding Pocket of Aminoacylase-1‡

The aminoacylase-1/metallopeptidase 20 (Acy1/M20) family features several l-aminoacylases useful in biocatalysis. Mammalian Acy1, in particular, has been applied in racemic resolution and reverse hydrolysis. Despite recent advances in our understanding of the active site architecture and functioning, determinants of Acy1 substrate specificity have remained uncharted. Comparison to bacterial homologues points to a sterically more restricted acyl-binding pocket for Acy1. Here we sought to map characteristics of the acyl-binding pocket of human and porcine Acy1. Toward this end, we determined Michaelis constants for an analogue series of aliphatic N-acyl- l-methionine substrates and translated the values into three-dimensional quantitative structure-activity relationship models employing the minimal topological difference-partial least square method. The QSAR models for the two enzymes suggest overall similar binding pockets in the acetyl-binding portion and indicate a general preference for straight-chain acyl moieties. Embedding of the QSAR map for human Acy1 in the structure of its metal-binding domain associates the side chain of Ile177 with limited acyl chain elongation which was not observed for the porcine enzyme. The topological model further supports roles of Thr347 and Leu372, which are both conserved in the porcine enzyme, in restricting acyl chain branching at the alpha- and beta-positions, respectively. Mutational analyses confirmed our predictions for Thr347 and Leu372. Moreover, the T347S variant of human Acy1 exhibited markedly increased catalytic efficiency against N-benzoylamino acids, demonstrating the potential for engineering of substrate specificity in Acy1. We discuss the more general application of the employed procedure for protein design.