Published in PLoS One on April 18, 2007
Regulation and cellular roles of ubiquitin-specific deubiquitinating enzymes. Annu Rev Biochem (2009) 6.23
Protein partners of deubiquitinating enzymes. Biochem J (2008) 2.15
Corruption of innate immunity by bacterial proteases. J Innate Immun (2009) 1.96
The E Block motif is associated with Legionella pneumophila translocated substrates. Cell Microbiol (2010) 1.51
Large-scale identification of Legionella pneumophila Dot/Icm substrates that modulate host cell vesicle trafficking pathways. Cell Microbiol (2008) 1.47
E3 ubiquitin ligase activity and targeting of BAT3 by multiple Legionella pneumophila translocated substrates. Infect Immun (2010) 1.34
Ubiquitin C-terminal electrophiles are activity-based probes for identification and mechanistic study of ubiquitin conjugating machinery. ACS Chem Biol (2009) 1.16
Ubiquitin and ubiquitin-modified proteins activate the Pseudomonas aeruginosa T3SS cytotoxin, ExoU. Mol Microbiol (2011) 1.13
An improved SUMO fusion protein system for effective production of native proteins. Protein Sci (2008) 1.03
Epstein-barr virus encodes three bona fide ubiquitin-specific proteases. J Virol (2008) 1.01
Characterization of selective ubiquitin and ubiquitin-like protease inhibitors using a fluorescence-based multiplex assay format. Assay Drug Dev Technol (2010) 1.00
Identification of ubiquitin-specific protease 9X (USP9X) as a deubiquitinase acting on ubiquitin-peroxin 5 (PEX5) thioester conjugate. J Biol Chem (2012) 0.96
Structural basis of substrate recognition by a bacterial deubiquitinase important for dynamics of phagosome ubiquitination. Proc Natl Acad Sci U S A (2015) 0.90
Trojan horse strategies used by pathogens to influence the small ubiquitin-like modifier (SUMO) system of host eukaryotic cells. J Innate Immun (2012) 0.89
Strategies for the identification of novel inhibitors of deubiquitinating enzymes. Biochem Soc Trans (2008) 0.85
A novel Ecotin-Ubiquitin-Tag (ECUT) for efficient, soluble peptide production in the periplasm of Escherichia coli. Microb Cell Fact (2009) 0.85
Substrate specificity of the ubiquitin and Ubl proteases. Cell Res (2016) 0.80
The Molecular Basis for Ubiquitin and Ubiquitin-like Specificities in Bacterial Effector Proteases. Mol Cell (2016) 0.79
Evaluation of selected binding domains for the analysis of ubiquitinated proteomes. J Am Soc Mass Spectrom (2013) 0.78
Ubiquitin C-terminal hydrolases cleave isopeptide- and peptide-linked ubiquitin from structured proteins but do not edit ubiquitin homopolymers. Biochem J (2015) 0.78
Activity, specificity, and probe design for the smallpox virus protease K7L. J Biol Chem (2012) 0.77
Novel ubiquitin-derived high affinity binding proteins with tumor targeting properties. J Biol Chem (2014) 0.76
Tail-Anchored Inner Membrane Protein ElaB Increases Resistance to Stress While Reducing Persistence in Escherichia coli. J Bacteriol (2017) 0.75
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res (1997) 175.36
The complete genome sequence of Escherichia coli K-12. Science (1997) 84.27
MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform (2004) 72.40
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol (2006) 40.15
Protein sequence similarity searches using patterns as seeds. Nucleic Acids Res (1998) 23.87
The Jalview Java alignment editor. Bioinformatics (2004) 21.74
Modification of proteins by ubiquitin and ubiquitin-like proteins. Annu Rev Cell Dev Biol (2006) 10.74
A genomic and functional inventory of deubiquitinating enzymes. Cell (2005) 9.36
JPred: a consensus secondary structure prediction server. Bioinformatics (1998) 8.71
The 1.2-megabase genome sequence of Mimivirus. Science (2004) 8.37
Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T. Infect Immun (2003) 5.11
Evidence in the Legionella pneumophila genome for exploitation of host cell functions and high genome plasticity. Nat Genet (2004) 4.93
Yersinia YopJ acetylates and inhibits kinase activation by blocking phosphorylation. Science (2006) 4.71
Mechanism and function of deubiquitinating enzymes. Biochim Biophys Acta (2004) 4.54
Cloning and expression of the cDNA for E6-AP, a protein that mediates the interaction of the human papillomavirus E6 oncoprotein with p53. Mol Cell Biol (1993) 4.04
An extensive repertoire of type III secretion effectors in Escherichia coli O157 and the role of lambdoid phages in their dissemination. Proc Natl Acad Sci U S A (2006) 3.89
Chemistry-based functional proteomics reveals novel members of the deubiquitinating enzyme family. Chem Biol (2002) 3.43
Rickettsiae and Chlamydiae: evidence of horizontal gene transfer and gene exchange. Trends Genet (1999) 2.87
How to become a uropathogen: comparative genomic analysis of extraintestinal pathogenic Escherichia coli strains. Proc Natl Acad Sci U S A (2006) 2.75
The Fungal Genetics Stock Center: from molds to molecules. Adv Appl Microbiol (2003) 2.48
Crystal structure of the human ubiquitin-like protein NEDD8 and interactions with ubiquitin pathway enzymes. J Biol Chem (1998) 2.44
Metabolism of the polyubiquitin degradation signal: structure, mechanism, and role of isopeptidase T. Biochemistry (1995) 2.31
The papain-like protease from the severe acute respiratory syndrome coronavirus is a deubiquitinating enzyme. J Virol (2005) 2.27
Acetylation of MEK2 and I kappa B kinase (IKK) activation loop residues by YopJ inhibits signaling. Proc Natl Acad Sci U S A (2006) 2.25
The structure of the APPBP1-UBA3-NEDD8-ATP complex reveals the basis for selective ubiquitin-like protein activation by an E1. Mol Cell (2003) 2.25
Exploitation of eukaryotic ubiquitin signaling pathways by effectors translocated by bacterial type III and type IV secretion systems. PLoS Pathog (2007) 2.14
Cloning and enzymatic analysis of 22 novel human ubiquitin-specific proteases. Biochem Biophys Res Commun (2004) 2.13
Structural basis for SENP2 protease interactions with SUMO precursors and conjugated substrates. Nat Struct Mol Biol (2006) 2.07
A novel superfamily of predicted cysteine proteases from eukaryotes, viruses and Chlamydia pneumoniae. Trends Biochem Sci (2000) 2.01
SseL, a Salmonella deubiquitinase required for macrophage killing and virulence. Proc Natl Acad Sci U S A (2007) 1.99
Evolutionary lines of cysteine peptidases. Biol Chem (2001) 1.90
Specific and covalent targeting of conjugating and deconjugating enzymes of ubiquitin-like proteins. Mol Cell Biol (2004) 1.86
Yersinia virulence factor YopJ acts as a deubiquitinase to inhibit NF-kappa B activation. J Exp Med (2005) 1.85
A deubiquitinating activity is conserved in the large tegument protein of the herpesviridae. J Virol (2005) 1.85
The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains. Genome Biol (2006) 1.82
The MEROPS database as a protease information system. J Struct Biol (2001) 1.78
Function of the Yersinia effector YopJ. Curr Opin Microbiol (2002) 1.68
Conservation in the mechanism of Nedd8 activation by the human AppBp1-Uba3 heterodimer. J Biol Chem (2003) 1.68
SUSP1 antagonizes formation of highly SUMO2/3-conjugated species. J Cell Biol (2006) 1.67
Saccharomyces cerevisiae SMT4 encodes an evolutionarily conserved protease with a role in chromosome condensation regulation. Genetics (2001) 1.65
Identification and characterization of DEN1, a deneddylase of the ULP family. J Biol Chem (2003) 1.62
African swine fever virus protease, a new viral member of the SUMO-1-specific protease family. J Biol Chem (2001) 1.60
Deubiquitinating function of adenovirus proteinase. J Virol (2002) 1.55
Structural basis of NEDD8 ubiquitin discrimination by the deNEDDylating enzyme NEDP1. EMBO J (2005) 1.48
Characterization of the Xanthomonas AvrXv4 effector, a SUMO protease translocated into plant cells. Mol Plant Microbe Interact (2004) 1.42
Genes homologous to ubiquitin-conjugating proteins and eukaryotic transcription factor SII in African swine fever virus. Virology (1992) 1.37
Chlamydia trachomatis-derived deubiquitinating enzymes in mammalian cells during infection. Mol Microbiol (2006) 1.30
Type III effector proteins from the plant pathogen Xanthomonas and their role in the interaction with the host plant. J Plant Physiol (2005) 1.29
Gly-Gly-X, a novel consensus sequence for the proteolytic processing of viral and cellular proteins. J Biol Chem (1989) 1.16
Solution structure of Urm1 and its implications for the origin of protein modifiers. Proc Natl Acad Sci U S A (2006) 1.14
A ubiquitin conjugating enzyme encoded by African swine fever virus. EMBO J (1992) 1.08
A functional screen identifies lateral transfer of beta-glucuronidase (gus) from bacteria to fungi. Mol Biol Evol (2004) 1.06
Characterization of the cysteine protease domain of Semliki Forest virus replicase protein nsP2 by in vitro mutagenesis. FEBS Lett (2006) 0.90
Chemistry-based functional proteomics: mechanism-based activity-profiling tools for ubiquitin and ubiquitin-like specific proteases. J Proteome Res (2004) 0.90
Structural aspects of recently discovered viral deubiquitinating activities. Biol Chem (2006) 0.89
Substrate specificity of adenovirus protease. Virus Res (2002) 0.89
CX3CR1-mediated dendritic cell access to the intestinal lumen and bacterial clearance. Science (2005) 8.97
A membrane protein required for dislocation of misfolded proteins from the ER. Nature (2004) 5.39
UNC93B1 delivers nucleotide-sensing toll-like receptors to endolysosomes. Nature (2008) 5.15
Haploid genetic screens in human cells identify host factors used by pathogens. Science (2009) 4.91
The Angelman Syndrome protein Ube3A regulates synapse development by ubiquitinating arc. Cell (2010) 4.72
Regulation of monoubiquitinated PCNA by DUB autocleavage. Nat Cell Biol (2006) 4.67
T-cell engagement of dendritic cells rapidly rearranges MHC class II transport. Nature (2002) 3.93
Glyburide inhibits the Cryopyrin/Nalp3 inflammasome. J Cell Biol (2009) 3.85
The interaction between the ER membrane protein UNC93B and TLR3, 7, and 9 is crucial for TLR signaling. J Cell Biol (2007) 3.72
Proteolytic cleavage in an endolysosomal compartment is required for activation of Toll-like receptor 9. Nat Immunol (2008) 3.61
Chemistry-based functional proteomics reveals novel members of the deubiquitinating enzyme family. Chem Biol (2002) 3.43
Sortagging: a versatile method for protein labeling. Nat Chem Biol (2007) 3.39
Road to ruin: targeting proteins for degradation in the endoplasmic reticulum. Science (2011) 3.19
Multiprotein complexes that link dislocation, ubiquitination, and extraction of misfolded proteins from the endoplasmic reticulum membrane. Proc Natl Acad Sci U S A (2005) 3.01
A microengraving method for rapid selection of single cells producing antigen-specific antibodies. Nat Biotechnol (2006) 2.94
An unconventional role for miRNA: let-7 activates Toll-like receptor 7 and causes neurodegeneration. Nat Neurosci (2012) 2.90
The known unknowns of antigen processing and presentation. Nat Rev Immunol (2008) 2.85
Structure of the ubiquitin hydrolase UCH-L3 complexed with a suicide substrate. J Biol Chem (2004) 2.75
Pannexin-1 is required for ATP release during apoptosis but not for inflammasome activation. J Immunol (2011) 2.67
Crystal structure of the boronic acid-based proteasome inhibitor bortezomib in complex with the yeast 20S proteasome. Structure (2006) 2.56
Neuronal loss and brain atrophy in mice lacking cathepsins B and L. Proc Natl Acad Sci U S A (2002) 2.54
CD8α(+) dendritic cells are the critical source of interleukin-12 that controls acute infection by Toxoplasma gondii tachyzoites. Immunity (2011) 2.50
A deubiquitinating enzyme encoded by HSV-1 belongs to a family of cysteine proteases that is conserved across the family Herpesviridae. Mol Cell (2005) 2.43
Parasite stage-specific recognition of endogenous Toxoplasma gondii-derived CD8+ T cell epitopes. J Infect Dis (2008) 2.40
SEL1L nucleates a protein complex required for dislocation of misfolded glycoproteins. Proc Natl Acad Sci U S A (2008) 2.38
Global gene disruption in human cells to assign genes to phenotypes by deep sequencing. Nat Biotechnol (2011) 2.23
Zinc-finger protein A20, a regulator of inflammation and cell survival, has de-ubiquitinating activity. Biochem J (2004) 2.23
A single protease, Apg4B, is specific for the autophagy-related ubiquitin-like proteins GATE-16, MAP1-LC3, GABARAP, and Apg8L. J Biol Chem (2003) 2.22
A role for N-glycanase in the cytosolic turnover of glycoproteins. EMBO J (2003) 2.18
SEL1L, the homologue of yeast Hrd3p, is involved in protein dislocation from the mammalian ER. J Cell Biol (2006) 2.13
Chemical probes for the rapid detection of Fatty-acylated proteins in Mammalian cells. J Am Chem Soc (2007) 2.10
Differential dependence of CD4+CD25+ regulatory and natural killer-like T cells on signals leading to NF-kappaB activation. Proc Natl Acad Sci U S A (2004) 2.09
Behavioral responses of epidermal Langerhans cells in situ to local pathological stimuli. J Invest Dermatol (2006) 2.05
Concurrent detection of secreted products from human lymphocytes by microengraving: cytokines and antigen-reactive antibodies. Clin Immunol (2008) 2.03
Accessory molecules for Toll-like receptors and their function. Nat Rev Immunol (2012) 2.00
Phosphorylation of NLRC4 is critical for inflammasome activation. Nature (2012) 1.92
Mechanisms, biology and inhibitors of deubiquitinating enzymes. Nat Chem Biol (2007) 1.90
Specific and covalent targeting of conjugating and deconjugating enzymes of ubiquitin-like proteins. Mol Cell Biol (2004) 1.86
A deubiquitinating activity is conserved in the large tegument protein of the herpesviridae. J Virol (2005) 1.85
Ubiquitin-like proteins. Annu Rev Biochem (2012) 1.84
The otubain YOD1 is a deubiquitinating enzyme that associates with p97 to facilitate protein dislocation from the ER. Mol Cell (2009) 1.82
Antigen presentation and the ubiquitin-proteasome system in host-pathogen interactions. Adv Immunol (2006) 1.78
Activity probe for in vivo profiling of the specificity of proteasome inhibitor bortezomib. Nat Methods (2005) 1.78
Structure of a herpesvirus-encoded cysteine protease reveals a unique class of deubiquitinating enzymes. Mol Cell (2007) 1.75
Transnuclear mice with predefined T cell receptor specificities against Toxoplasma gondii obtained via SCNT. Science (2010) 1.74
Signal peptide peptidase is required for dislocation from the endoplasmic reticulum. Nature (2006) 1.73
XBP-1 regulates signal transduction, transcription factors and bone marrow colonization in B cells. EMBO J (2009) 1.72
Identification of proteins associated with murine cytomegalovirus virions. J Virol (2004) 1.72
Loss of Usp14 results in reduced levels of ubiquitin in ataxia mice. J Neurochem (2005) 1.71
Ubiquitination, ubiquitin-like modifiers, and deubiquitination in viral infection. Cell Host Microbe (2009) 1.69
Protein quality control in the ER: balancing the ubiquitin checkbook. Trends Cell Biol (2011) 1.68
Analysis of protease activity in live antigen-presenting cells shows regulation of the phagosomal proteolytic contents during dendritic cell activation. J Exp Med (2002) 1.64
Site-specific N- and C-terminal labeling of a single polypeptide using sortases of different specificity. J Am Chem Soc (2009) 1.63
Murine polyomavirus requires the endoplasmic reticulum protein Derlin-2 to initiate infection. J Virol (2006) 1.62
Activity-based ubiquitin-specific protease (USP) profiling of virus-infected and malignant human cells. Proc Natl Acad Sci U S A (2004) 1.59
Making and breaking peptide bonds: protein engineering using sortase. Angew Chem Int Ed Engl (2011) 1.58
Screen for ISG15-crossreactive deubiquitinases. PLoS One (2007) 1.57
The mouse polyubiquitin gene UbC is essential for fetal liver development, cell-cycle progression and stress tolerance. EMBO J (2007) 1.56
Live imaging of cysteine-cathepsin activity reveals dynamics of focal inflammation, angiogenesis, and polyp growth. PLoS One (2008) 1.55
A glycosylated type I membrane protein becomes cytosolic when peptide: N-glycanase is compromised. EMBO J (2004) 1.53
Competition by inhibitory oligonucleotides prevents binding of CpG to C-terminal TLR9. Eur J Immunol (2011) 1.52
High-molecular-weight protein (pUL48) of human cytomegalovirus is a competent deubiquitinating protease: mutant viruses altered in its active-site cysteine or histidine are viable. J Virol (2006) 1.52
A functional proteomics approach links the ubiquitin-related modifier Urm1 to a tRNA modification pathway. Proc Natl Acad Sci U S A (2008) 1.51
Asparagine endopeptidase is not essential for class II MHC antigen presentation but is required for processing of cathepsin L in mice. J Immunol (2005) 1.50
Zwitterionic polysaccharides stimulate T cells by MHC class II-dependent interactions. J Immunol (2002) 1.50
Identification of host cell factors required for intoxication through use of modified cholera toxin. J Cell Biol (2011) 1.47
The caspase-like sites of proteasomes, their substrate specificity, new inhibitors and substrates, and allosteric interactions with the trypsin-like sites. J Biol Chem (2003) 1.46
Dissection of the dislocation pathway for type I membrane proteins with a new small molecule inhibitor, eeyarestatin. Mol Biol Cell (2004) 1.44
Discovery of CD8+ T cell epitopes in Chlamydia trachomatis infection through use of caged class I MHC tetramers. Proc Natl Acad Sci U S A (2008) 1.43
Site-specific protein labeling via sortase-mediated transpeptidation. Curr Protoc Protein Sci (2009) 1.43
Viral modulation of antigen presentation: manipulation of cellular targets in the ER and beyond. Immunol Rev (2005) 1.43
Using a small molecule inhibitor of peptide: N-glycanase to probe its role in glycoprotein turnover. Chem Biol (2004) 1.42
Quality and quantity control at the endoplasmic reticulum. Curr Opin Cell Biol (2010) 1.42
Effects of PS-341 on the activity and composition of proteasomes in multiple myeloma cells. Cancer Res (2005) 1.39
Visualization of the ER-to-cytosol dislocation reaction of a type I membrane protein. EMBO J (2002) 1.39
Rapid turnover of unspliced Xbp-1 as a factor that modulates the unfolded protein response. J Biol Chem (2005) 1.39
Preparation of unnatural N-to-N and C-to-C protein fusions. Proc Natl Acad Sci U S A (2012) 1.38
Granulin is a soluble cofactor for toll-like receptor 9 signaling. Immunity (2011) 1.36
Kaposi's sarcoma-associated herpesvirus K3 utilizes the ubiquitin-proteasome system in routing class major histocompatibility complexes to late endocytic compartments. J Virol (2002) 1.36
Preferred in vivo ubiquitination sites. Bioinformatics (2004) 1.36
The CD8 T-cell response against murine gammaherpesvirus 68 is directed toward a broad repertoire of epitopes from both early and late antigens. J Virol (2008) 1.35
Lipid modification of proteins through sortase-catalyzed transpeptidation. J Am Chem Soc (2008) 1.34
Enzymatic blockade of the ubiquitin-proteasome pathway. PLoS Biol (2011) 1.33
A closer look at proteolysis and MHC-class-II-restricted antigen presentation. Curr Opin Immunol (2002) 1.32
Cellular internalization of cytolethal distending toxin: a new end to a known pathway. Cell Microbiol (2005) 1.32
A straight path to circular proteins. J Biol Chem (2009) 1.31
Chlamydia trachomatis-derived deubiquitinating enzymes in mammalian cells during infection. Mol Microbiol (2006) 1.30
The human cytomegalovirus US10 gene product delays trafficking of major histocompatibility complex class I molecules. J Virol (2002) 1.28
Fungal recognition is mediated by the association of dectin-1 and galectin-3 in macrophages. Proc Natl Acad Sci U S A (2011) 1.28
Helicobacter pylori cytotoxin-associated gene A (CagA) subverts the apoptosis-stimulating protein of p53 (ASPP2) tumor suppressor pathway of the host. Proc Natl Acad Sci U S A (2011) 1.27
Membrane-specific, host-derived factors are required for US2- and US11-mediated degradation of major histocompatibility complex class I molecules. J Biol Chem (2001) 1.27
Tubulation of class II MHC compartments is microtubule dependent and involves multiple endolysosomal membrane proteins in primary dendritic cells. J Immunol (2007) 1.27
Chemistry in living cells: detection of active proteasomes by a two-step labeling strategy. Angew Chem Int Ed Engl (2003) 1.25
Differential regulation of effector- and central-memory responses to Toxoplasma gondii Infection by IL-12 revealed by tracking of Tgd057-specific CD8+ T cells. PLoS Pathog (2010) 1.25
Profiling antibody responses by multiparametric analysis of primary B cells. Proc Natl Acad Sci U S A (2008) 1.25
Mechanism-based probe for the analysis of cathepsin cysteine proteases in living cells. ACS Chem Biol (2006) 1.25
Site-specific C-terminal and internal loop labeling of proteins using sortase-mediated reactions. Nat Protoc (2013) 1.25