Cited by 367Bacterial Genetics and BiotechnologyBiochemical and Structural CharacterizationEnzyme Structure and Function

The DOI matches its Crossref record; 73 of the 73 references it cites were found in a registry or an index.

Evolutionary history, structural features and biochemical diversity of the NlpC/P60 superfamily of enzymes

Open access

Anantharaman, Vivek, Aravind, L·2003·Genome Biology

DOI 10.1186/gb-2003-4-2-r11PMC PMC151301

Open this paper in CoChat — free account Open PDF

Abstract

BACKGROUND: Peptidoglycan is hydrolyzed by a diverse set of enzymes during bacterial growth, development and cell division. The N1pC/P60 proteins define a family of cell-wall peptidases that are widely represented in various bacterial lineages. Currently characterized members are known to hydrolyze D-gamma-glutamyl-meso-diaminopimelate or N-acetylmuramate-L-alanine linkages. RESULTS: Detailed analysis of the N1pC/P60 peptidases showed that these proteins define a large superfamily encompassing several diverse groups of proteins. In addition to the well characterized P60-like proteins, this superfamily includes the AcmB/LytN and YaeF/YiiX families of bacterial proteins, the amidase domain of bacterial and kinetoplastid glutathionylspermidine synthases (GSPSs), and several proteins from eukaryotes, phages, poxviruses, positive-strand RNA viruses, and certain archaea. The eukaryotic members include lecithin retinol acyltransferase (LRAT), nematode developmental regulator Egl-26, and candidate tumor suppressor H-rev107. These eukaryotic proteins, along with the bacterial YaeF/poxviral G6R family, show a circular permutation of the catalytic domain. We identified three conserved residues, namely a cysteine, a histidine and a polar residue, that are involved in the catalytic activities of this superfamily. Evolutionary analysis of this superfamily shows that it comprises four major families, with diverse domain architectures in each of them. CONCLUSIONS: Several related, but distinct, catalytic activities, such as murein degradation, acyl transfer and amide hydrolysis, have emerged in the N1pC/P60 superfamily. The three conserved catalytic residues of this superfamily are shown to be equivalent to the catalytic triad of the papain-like thiol peptidases. The predicted structural features indicate that the N1pC/P60 enzymes contain a fold similar to the papain-like peptidases, transglutaminases and arylamine acetyltransferases.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1186/gb-2003-4-2-r11

Cites

73 of 73 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
PHYLIP-Phylogeny inference package (Version 3.2)
Felsenstein, J. (1989) · Cladistics · Cited by 17,682
MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures
Kraulis, P. J. (1991) · Journal of Applied Crystallography · doi:10.1107/s0021889891004399 · Cited by 14,011
SWISS‐MODEL and the Swiss‐Pdb Viewer: An environment for comparative protein modeling
Guex, N., & Peitsch, M. C. (1997) · Electrophoresis · doi:10.1002/elps.1150181505 · Cited by 11,312
T-coffee: a novel method for fast and accurate multiple sequence alignment 1 1Edited by J. Thornton
Notredame, C., Higgins, D. G., & Heringa, J. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.4042 · Cited by 6,964
Brock Biology of Microorganisms
Madigan, M. T., Bender, K. S., Buckley, D. H., Sattley, W. M., & Stahl, D. A. (1996) · Cited by 5,759
Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites
Nielsen, H., Engelbrecht, J., Brunak, S., & von HEIJNE, G. (1997) · Protein Engineering Design and Selection · doi:10.1093/protein/10.1.1 · Cited by 5,343
Protein Structure Comparison by Alignment of Distance Matrices
Holm, L., & Sander, C. (1993) · Journal of Molecular Biology · doi:10.1006/jmbi.1993.1489 · Cited by 3,984 · cited 1×
“Searches of the PDB database with query structures was conducted using the DALI program [70,71].”
Method
Prediction of Protein Secondary Structure at Better than 70% Accuracy
Rost, B., & Sander, C. (1993) · Journal of Molecular Biology · doi:10.1006/jmbi.1993.1413 · Cited by 2,927
Membrane protein structure prediction
von HEIJNE, G. (1992) · Journal of Molecular Biology · doi:10.1016/0022-2836(92)90934-c · Cited by 1,679

Show all 73 references

Research works printed but not linked: 1

Moat AG, Foster JW, Eds: Microbial Physiology. 2002, New York: John Wiley, 4th

Sorted by citations

Type VI secretion delivers bacteriolytic effectors to target cells
Russell, A. B., Hood, R. D., Bui, N. K., LeRoux, M., Vollmer, W., & Mougous, J. D. (2011) · Nature · doi:10.1038/nature10244 · Cited by 754
Evolutionary genomics of nucleo-cytoplasmic large DNA viruses
Iyer, L. M., Balaji, S., Koonin, E. V., & Aravind, L. (2006) · Virus Research · doi:10.1016/j.virusres.2006.01.009 · Cited by 585
Self-citation
Polymorphic toxin systems: Comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics
Zhang, D., de Souza, R. F., Anantharaman, V., Iyer, L. M., & Aravind, L. (2012) · Biology Direct · doi:10.1186/1745-6150-7-18 · Cited by 530
Self-citation
Retinol and retinyl esters: biochemistry and physiology
O'Byrne, S. M., & Blaner, W. S. (2013) · Journal of Lipid Research · doi:10.1194/jlr.r037648 · Cited by 378
Endolysins as Antimicrobials
Nelson, D. C., Schmelcher, M., Rodríguez‐Rubio, L., Klumpp, J., Pritchard, D. G., Dong, S., & Donovan, D. M. (2012) · Advances in virus research · doi:10.1016/b978-0-12-394438-2.00007-4 · Cited by 375
Lecithin-retinol acyltransferase is essential for accumulation of all-trans-retinyl esters in the eye and in the liver
Batten, M. L., Imanishi, Y., Maeda, T., Tu, D. C., Moise, A. R., Bronson, D., Possin, D., Van Gelder, R. N., Baehr, W., & Palczewski, K. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m312410200 · Cited by 368
Chemistry of the Retinoid (Visual) Cycle
Kiser, P. D., Golczak, M., & Palczewski, K. (2014) · Chemical Reviews · doi:10.1021/cr400107q · Cited by 353
Cell Wall Hydrolases in Bacteria: Insight on the Diversity of Cell Wall Amidases, Glycosidases and Peptidases Toward Peptidoglycan
Vermassen, A., Léroy, S., Talòn, R., Provot, C., Popowska, M., & Desvaux, M. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.00331 · Cited by 337
Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging
Iyer, L. M. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh828 · Cited by 327
A widespread bacterial type VI secretion effector superfamily identified using a heuristic approach
Russell, A. B., Singh, P., Brittnacher, M., Bui, N., Hood, R. D., Carl, M. A., Agnello, D. M., Schwarz, S., Goodlett, D., Vollmer, W., et al. (2012) · Cell Host and Microbe · doi:10.1016/j.chom.2012.04.007 · Cited by 310
Bacterial killing via a type IV secretion system
de Souza, D. P., Oka, G. U., Alvarez‐Martinez, C. E., Bisson‐Filho, A. W., Dunger, G., Hobeika, L., Cavalcante, N. G. S., Alegria, M. C., Barbosa, L. R. S., Salinas, R. K., et al. (2015) · Nature Communications · doi:10.1038/ncomms7453 · Cited by 275
Listeria monocytogenesSurface Proteins: from Genome Predictions to Function
Bierne, H., & Cossart, P. (2007) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00039-06 · Cited by 235
Metabolism of endocannabinoids and related N ‐acylethanolamines: Canonical and alternative pathways
Ueda, N., Tsuboi, K., & Uyama, T. (2013) · FEBS Journal · doi:10.1111/febs.12152 · Cited by 242
Three redundant murein endopeptidases catalyse an essential cleavage step in peptidoglycan synthesis of E scherichia coli K 12
Singh, S. K., SaiSree, L., Amrutha, R. N., & Reddy, M. (2012) · Molecular Microbiology · doi:10.1111/mmi.12058 · Cited by 214
Functional metagenomic discovery of bacterial effectors in the human microbiome and isolation of commendamide, a GPCR G2A/132 agonist
Cohen, L. J., Kang, H., Chu, J., Huang, Y.-H., Gordon, E. A., Reddy, B. V. B., Ternei, M. A., Craig, J. W., & Brady, S. F. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1508737112 · Cited by 208
The different shapes of cocci
Zapun, A., Vernet, T., & Pinho, M. G. (2008) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.2007.00098.x · Cited by 194
Key enzymes of the retinoid (visual) cycle in vertebrate retina
Kiser, P. D., Golczak, M., Maeda, A., & Palczewski, K. (2012) · Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids · doi:10.1016/j.bbalip.2011.03.005 · Cited by 177
A Mycobacterial Enzyme Essential for Cell Division Synergizes with Resuscitation-Promoting Factor
Hett, E. C., Chao, M. C., Deng, L. L., & Rubin, E. J. (2008) · PLoS Pathogens · doi:10.1371/journal.ppat.1000001 · Cited by 169
N-acylethanolamine metabolism with special reference to N-acylethanolamine-hydrolyzing acid amidase (NAAA)
Ueda, N., Tsuboi, K., & Uyama, T. (2010) · Progress in Lipid Research · doi:10.1016/j.plipres.2010.02.003 · Cited by 166
New insights into the pneumococcal fratricide: relationship to clumping and identification of a novel immunity factor
Håvarstein, L. S., Martin, B., Johnsborg, O., Granadel, C., & Claverys, J. (2005) · Molecular Microbiology · doi:10.1111/j.1365-2958.2005.05021.x · Cited by 163
The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like β-grasp domains
Iyer, L. M., Burroughs, A. M., & Aravind, L. (2006) · Genome biology · doi:10.1186/gb-2006-7-7-r60 · Cited by 161
Self-citation
Elucidation of ataxin-3 and ataxin-7 function by integrative bioinformatics
Scheel, H. (2003) · Human Molecular Genetics · doi:10.1093/hmg/ddg297 · Cited by 159
A partner for the resuscitation‐promoting factors of Mycobacterium tuberculosis
Hett, E. C., Chao, M. C., Steyn, A. J. C., Fortune, S. M., Deng, L. L., & Rubin, E. J. (2007) · Molecular Microbiology · doi:10.1111/j.1365-2958.2007.05945.x · Cited by 162
Amidase domains from bacterial and phage autolysins define a family of γ-d,l-glutamate-specific amidohydrolases
Rigden, D. J., Jedrzejas, M. J., & Galperin, M. Y. (2003) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(03)00062-8 · Cited by 158
Discovery and Characterization of a Ca2+-independent Phosphatidylethanolamine N-Acyltransferase Generating the Anandamide Precursor and Its Congeners
Jin, X.-H., Okamoto, Y., Morishita, J., Tsuboi, K., Tonai, T., & Ueda, N. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m606369200 · Cited by 155
Essential PcsB putative peptidoglycan hydrolase interacts with the essential FtsX Spn cell division protein in Streptococcus pneumoniae D39
Sham, L., Barendt, S. M., Kopecky, K. E., & Winkler, M. E. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1108323108 · Cited by 164
Defective cell wall synthesis in Streptococcus pneumoniae R6 depleted for the essential PcsB putative murein hydrolase or the VicR (YycF) response regulator
Ng, W., Kazmierczak, K. M., & Winkler, M. E. (2004) · Molecular Microbiology · doi:10.1111/j.1365-2958.2004.04196.x · Cited by 146
A Palmitoylation Switch Mechanism in the Regulation of the Visual Cycle
Xue, L., Gollapalli, D. R., Maiti, P., Jahng, W. J., & Rando, R. R. (2004) · Cell · doi:10.1016/j.cell.2004.05.016 · Cited by 143
Coiled-coil protein composition of 22 proteomes – differences and common themes in subcellular infrastructure and traffic control
Rose, A., Schraegle, S. J., Stahlberg, E. A., & Meier, I. (2005) · BMC Evolutionary Biology · doi:10.1186/1471-2148-5-66 · Cited by 138
Choline-Binding Protein D (CbpD) inStreptococcus pneumoniaeIs Essential for Competence-Induced Cell Lysis
Kausmally, L., Johnsborg, O., Lunde, M., Knutsen, E., & Håvarstein, L. S. (2005) · Journal of Bacteriology · doi:10.1128/jb.187.13.4338-4345.2005 · Cited by 130
Envelope stress responses defend against type six secretion system attacks independently of immunity proteins
Hersch, S. J., Watanabe, N., Stietz, M. S., Manera, K., Kamal, F., Burkinshaw, B. J., Lam, L., Pun, A., Li, M., Savchenko, A. V., et al. (2020) · Nature Microbiology · doi:10.1038/s41564-020-0672-6 · Cited by 122
Structure of the Jab1/MPN Domain and Its Implications for Proteasome Function
Tran, H. J. T. T., Allen, M. D., Löwe, J., & Bycroft, M. (2003) · Biochemistry · doi:10.1021/bi035033g · Cited by 125
A Single-Amino-Acid Change in Murine Norovirus NS1/2 Is Sufficient for Colonic Tropism and Persistence
Nice, T. J., Strong, D. W., McCune, B. T., Pohl, C. S., & Virgin, H. W. (2012) · Journal of Virology · doi:10.1128/jvi.01864-12 · Cited by 124
Enterococcus faecium secreted antigen A generates muropeptides to enhance host immunity and limit bacterial pathogenesis
Kim, B., Wang, Y.-C., Hespen, C. W., Espinosa, J., Salje, J., Rangan, K. J., Oren, D. A., Kang, J. Y., Pedicord, V. A., & Hang, H. C. (2019) · eLife · doi:10.7554/elife.45343 · Cited by 120
Bacterial Peptidoglycan-Degrading Enzymes and Their Impact on Host Muropeptide Detection
Humann, J., & Lenz, L. L. (2008) · Journal of Innate Immunity · doi:10.1159/000181181 · Cited by 120
Differential Proteomic Analysis of theBacillus anthracisSecretome: Distinct Plasmid and Chromosome CO2-Dependent Cross Talk Mechanisms Modulate Extracellular Proteolytic Activities
Chitlaru, T., Gat, O., Gozlan, Y., Ariel, N., & Avigdor Shafferman, C. (2006) · Journal of Bacteriology · doi:10.1128/jb.188.10.3551-3571.2006 · Cited by 117
Orthologous Gene Clusters and Taxon Signature Genes for Viruses of Prokaryotes
Kristensen, D. M., Waller, A. S., Yamada, T., Peer Bork, B., Mushegian, A. R., & Koonin, E. V. (2012) · Journal of Bacteriology · doi:10.1128/jb.01801-12 · Cited by 113
Enzymological studies on the biosynthesis of N-acylethanolamines
Ueda, N., Tsuboi, K., & Uyama, T. (2010) · Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids · doi:10.1016/j.bbalip.2010.08.010 · Cited by 112
Retinoids and Retinal Diseases
Kiser, P. D., & Palczewski, K. (2016) · Annual Review of Vision Science · doi:10.1146/annurev-vision-111815-114407 · Cited by 108
“Compared with classical NlpC/P60 enzymes in which the nucleophilic cysteine residue resides on the N terminus, LRATlike members are circularly permuted, with the catalytic cysteine relocated to the C-terminal end (Anantharaman & Aravind 2003).”
Amidoligases with ATP-grasp, glutamine synthetase-like and acetyltransferase-like domains: synthesis of novel metabolites and peptide modifications of proteins
Iyer, L. M., Abhiman, S., Burroughs, A. M., & Aravind, L. (2009) · Molecular BioSystems · doi:10.1039/b917682a · Cited by 108
Self-citation
Structure of a Peptidoglycan Amidase Effector Targeted to Gram-Negative Bacteria by the Type VI Secretion System
Chou, S., Bui, N. K., Russell, A. B., Lexa, K. W., Gardiner, T. E., LeRoux, M., Vollmer, W., & Mougous, J. D. (2012) · Cell Reports · doi:10.1016/j.celrep.2012.05.016 · Cited by 116
Cell Envelope of Corynebacteria: Structure and Influence on Pathogenicity
Burkovski, A. (2013) · ISRN Microbiology · doi:10.1155/2013/935736 · Cited by 104
Jumbo Phages: A Comparative Genomic Overview of Core Functions and Adaptions for Biological Conflicts
Iyer, L. M., Anantharaman, V., Krishnan, A., Burroughs, A. M., & Aravind, L. (2021) · Viruses · doi:10.3390/v13010063 · Cited by 104
Self-citation
Functional Analysis of the p40 and p75 Proteins from Lactobacillus casei BL23
Bäuerl, C., Pérez‐Martínez, G., Yan, F., Polk, D. B., & Monedero, V. (2010) · Microbial Physiology · doi:10.1159/000322233 · Cited by 117
Immunoglobulin-like domains on bacteriophage: weapons of modest damage?
Fraser, J. S., Maxwell, K. L., & Davidson, A. R. (2007) · Current Opinion in Microbiology · doi:10.1016/j.mib.2007.05.018 · Cited by 102
Synthetic Lethality of the lytE cwlO Genotype in Bacillus subtilis Is Caused by Lack of d , l -Endopeptidase Activity at the Lateral Cell Wall
Hashimoto, M., Ooiwa, S., & Sekiguchi, J. (2011) · Journal of Bacteriology · doi:10.1128/jb.05569-11 · Cited by 101
A Mycobacterial Operon Essential for Virulence In Vivo and Invasion and Intracellular Persistence in Macrophages
Gao, L., Pak, M. A., Kish, R., Kajihara, K. K., & Brown, E. J. (2006) · Infection and Immunity · doi:10.1128/iai.74.3.1757-1767.2006 · Cited by 100
Leishmania Trypanothione Synthetase-Amidase Structure Reveals a Basis for Regulation of Conflicting Synthetic and Hydrolytic Activities
Fyfe, P. K., Oza, S. L., Fairlamb, A. H., & Hunter, W. N. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m801850200 · Cited by 100
Mammalian enzymes responsible for the biosynthesis of N -acylethanolamines
Hussain, Z., Uyama, T., Tsuboi, K., & Ueda, N. (2017) · Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids · doi:10.1016/j.bbalip.2017.08.006 · Cited by 100
The global cysteine peptidase landscape in parasites
Atkinson, H. J., Babbitt, P. C., & Sajid, M. (2009) · Trends in Parasitology · doi:10.1016/j.pt.2009.09.006 · Cited by 97
The tumor suppressor gene H-Rev107 functions as a novel Ca2+-independent cytosolic phospholipase A1/2 of the thiol hydrolase type
Uyama, T., Morishita, J., Jin, X.-H., Okamoto, Y., Tsuboi, K., & Ueda, N. (2009) · Journal of Lipid Research · doi:10.1194/jlr.m800453-jlr200 · Cited by 84
Membrane alterations induced by nonstructural proteins of human norovirus
Doerflinger, S. Y., Cortese, M., Romero‐Brey, I., Menne, Z., Tubiana, T., Schenk, C., White, P. A., Bartenschlager, R. F. W., Bressanelli, S., Hansman, G. S., et al. (2017) · PLoS Pathogens · doi:10.1371/journal.ppat.1006705 · Cited by 84
Corynebacterium diphtheriae invasion-associated protein (DIP1281) is involved in cell surface organization, adhesion and internalization in epithelial cells
Ott, L., Höller, M., Gerlach, R. G., Hensel, M., Rheinlaender, J., Schäffer, T. E., & Burkovski, A. (2010) · BMC Microbiology · doi:10.1186/1471-2180-10-2 · Cited by 83
Characterization of the human tumor suppressors TIG3 and HRASLS2 as phospholipid-metabolizing enzymes
Uyama, T., Jin, X.-H., Tsuboi, K., Tonai, T., & Ueda, N. (2009) · Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids · doi:10.1016/j.bbalip.2009.07.001 · Cited by 80
Folds and activities of peptidoglycan amidases
Firczuk, M., & Bochtler, M. (2007) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.2007.00084.x · Cited by 81
Influences of Capsule on Cell Shape and Chain Formation of Wild-Type andpcsBMutants of Serotype 2Streptococcus pneumoniae
Barendt, S. M., Land, A. D., Sham, L., Ng, W., Tsui, H. T., Arnold, R. J., & Winkler, M. E. (2009) · Journal of Bacteriology · doi:10.1128/jb.01505-08 · Cited by 81
Lipoproteins in Gram-Positive Bacteria: Abundance, Function, Fitness
Nguyen, M., Matsuo, M., Niemann, S., Herrmann, M., & Götz, F. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.582582 · Cited by 82
Similar active sites in lysostaphins and D‐Ala‐D‐Ala metallopeptidases
Bochtler, M., Odintsov, S. G., Marcyjaniak, M., & Sabała, I. (2004) · Protein Science · doi:10.1110/ps.03515704 · Cited by 78
Structural Basis for the Acyltransferase Activity of Lecithin:Retinol Acyltransferase-like Proteins
Golczak, M., Kiser, P. D., Sears, A. E., Lodowski, D. T., Blaner, W. S., & Palczewski, K. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.361550 · Cited by 77
Characterization of a New Bacillus subtilis Peptidoglycan Hydrolase Gene, yvcE (Named cwlO), and the Enzymatic Properties of Its Encoded Protein
Yamaguchi, H., Furuhata, K., Fukushima, T., Yamamoto, H., & Sekiguchi, J. (2004) · Journal of Bioscience and Bioengineering · doi:10.1016/s1389-1723(04)00262-2 · Cited by 77
The MEROPS batch BLAST: A tool to detect peptidases and their non-peptidase homologues in a genome
Rawlings, N. D., & Morton, F. R. (2007) · Biochimie · doi:10.1016/j.biochi.2007.09.014 · Cited by 77
Cell Wall Hydrolases Affect Germination, Vegetative Growth, and Sporulation in Streptomyces coelicolor
Haiser, H. J., Yousef, M. R., & Elliot, M. A. (2009) · Journal of Bacteriology · doi:10.1128/jb.00767-09 · Cited by 76
Agrobacterium tumefaciens ExoR Controls Acid Response Genes and Impacts Exopolysaccharide Synthesis, Horizontal Gene Transfer, and Virulence Gene Expression
Heckel, B. C., Tomlinson, A. D., Morton, E. R., Choi, J.-H., & Fuqua, C. (2014) · Journal of Bacteriology · doi:10.1128/jb.01751-14 · Cited by 76
How Listeria monocytogenes organizes its surface for virulence
Carvalho, F., Sousa, S., & Cabanes, D. (2014) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2014.00048 · Cited by 79
Identification of multiple independent horizontal gene transfers into poxviruses using a comparative genomics approach
Bratke, K. A., & McLysaght, A. (2008) · BMC Evolutionary Biology · doi:10.1186/1471-2148-8-67 · Cited by 75
Structure of the Type VI Effector-Immunity Complex (Tae4-Tai4) Provides Novel Insights into the Inhibition Mechanism of the Effector by Its Immunity Protein*
Zhang, H., Zhang, H., Gao, Z., Wang, W., Liu, G., Xu, J., Su, X., & Dong, Y. (2013) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.434357 · Cited by 75
The Composition and Structure of Biofilms Developed by Propionibacterium acnes Isolated from Cardiac Pacemaker Devices
Okuda, K.-I., Nagahori, R., Yamada, S., Sugimoto, S., Sato, C., Sato, M., Iwase, T., Hashimoto, K., & Mizunoe, Y. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.00182 · Cited by 74
A Family of T6SS Antibacterial Effectors Related to l,d-Transpeptidases Targets the Peptidoglycan
Sibinelli‐Sousa, S., Hespanhol, J. T., Nicastro, G. G., Matsuyama, B. Y., Mesnage, S., Patel, A. V., de Souza, R. F., Guzzo, C. R., & Bayer‐Santos, E. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.107813 · Cited by 70
The HRASLS (PLA/AT) subfamily of enzymes
Mardian, E. B., Bradley, R. M., & Duncan, R. E. (2015) · Journal of Biomedical Science · doi:10.1186/s12929-015-0210-7 · Cited by 72
New players in the fatty acyl ethanolamide metabolism
Rahman, I. A. S., Tsuboi, K., Uyama, T., & Ueda, N. (2014) · Pharmacological Research · doi:10.1016/j.phrs.2014.04.001 · Cited by 73
Oxidation–reduction signalling components in regulatory pathways of state transitions and photosystem stoichiometry adjustment in chloroplasts
Puthiyaveetil, S., Ibrahim, I. M., & Allen, J. F. (2011) · Plant Cell & Environment · doi:10.1111/j.1365-3040.2011.02349.x · Cited by 72
Simultaneous Deficiency of both MurA and p60 Proteins Generates a Rough Phenotype inListeria monocytogenes
Machata, S., Hain, T., Rohde, M., & Chakraborty, T. (2005) · Journal of Bacteriology · doi:10.1128/jb.187.24.8385-8394.2005 · Cited by 72
Manual classification strategies in the ECOD database
Cheng, H., Liao, Y., Schaeffer, R. D., & Grishin, N. V. (2015) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24818 · Cited by 71
Peptidoglycan Remodeling in Mycobacterium tuberculosis: Comparison of Structures and Catalytic Activities of RipA and RipB
Böth, D., Schneider, G., & Schnell, R. (2011) · Journal of Molecular Biology · doi:10.1016/j.jmb.2011.08.014 · Cited by 71
Molecular Basis for Vitamin A Uptake and Storage in Vertebrates
Chelstowska, S., Widjaja-Adhi, M., Silvaroli, J., & Golczak, M. (2016) · Nutrients · doi:10.3390/nu8110676 · Cited by 72
“Despite being evolutionary ‘young’, LRAT belongs to an ancient and diverse group of proteins called N1pC/P60 [107].”
BackgroundInfluential
On the reversibility of parasitism: adaptation to a free-living lifestyle via gene acquisitions in the diplomonad Trepomonas sp. PC1
Xu, F., Jerlström-Hultqvist, J., Kolísko, M., Simpson, A. G. B., Roger, A. J., Svärd, S. G., & Andersson, J. O. (2016) · BMC Biology · doi:10.1186/s12915-016-0284-z · Cited by 71
Structural Basis of Murein Peptide Specificity of a γ-D-Glutamyl-L-Diamino Acid Endopeptidase
Xu, Q., Sudek, S., McMullan, D., Miller, M. D., Geierstanger, B. H., Jones, D. H., Krishna, S. S., Spraggon, G., Bursalay, B., Abdubek, P., et al. (2009) · Structure · doi:10.1016/j.str.2008.12.008 · Cited by 69
Filling out the structural map of the NTF2-like superfamily
Eberhardt, R. Y., Chang, Y., Bateman, A. G., Murzin, A. G., Axelrod, H. L., Hwang, W. C., & Aravind, L. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-327 · Cited by 69
Self-citation
Solution NMR Structure of the NlpC/P60 Domain of Lipoprotein Spr from Escherichia coli: Structural Evidence for a Novel Cysteine Peptidase Catalytic Triad
Aramini, J. M., Rossi, P., Huang, Y. J., Zhao, L., Jiang, M., Maglaqui, M., Xiao, R., Locke, J. Y., Nair, R., Rost, B., et al. (2008) · Biochemistry · doi:10.1021/bi8010779 · Cited by 68
Structure of the γ- D -glutamyl- L -diamino acid endopeptidase YkfC fromBacillus cereusin complex with L -Ala-γ- D -Glu: insights into substrate recognition by NlpC/P60 cysteine peptidases
Xu, Q., Abdubek, P., Astakhova, T., Axelrod, H. L., Bakolitsa, C., Cai, X., Carlton, D. D., Chen, C., Chiu, H., Chiu, M., et al. (2010) · Acta Crystallographica Section F Structural Biology and Crystallization Communications · doi:10.1107/s1744309110021214 · Cited by 67
Carbohydrate recognition and lysis by bacterial peptidoglycan hydrolases
Alcorlo, M., Martínez‐Caballero, S., Molina, R., & Hermoso, J. A. (2017) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2017.01.001 · Cited by 66
Transglutaminases: part I—origins, sources, and biotechnological characteristics
Duarte, L. S., Matte, C. R., Bizarro, C. V., & Ayub, M. A. Z. (2020) · World Journal of Microbiology and Biotechnology · doi:10.1007/s11274-019-2791-x · Cited by 65
The molecular aspects of absorption and metabolism of carotenoids and retinoids in vertebrates
Widjaja‐Adhi, M. A. K., & Golczak, M. (2019) · Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids · doi:10.1016/j.bbalip.2019.158571 · Cited by 67
Structural Insights into the Effector – Immunity System Tse1/Tsi1 from Pseudomonas aeruginosa
Benz, J., Sendlmeier, C., Barends, T. R. M., & Meinhart, A. (2012) · PLoS ONE · doi:10.1371/journal.pone.0040453 · Cited by 63
Carotenoids provide the major antioxidant defence in the globally significant N 2 ‐fixing marine cyanobacterium Trichodesmium
Kelman, D., Ben‐Amotz, A., & Berman‐Frank, I. (2009) · Environmental Microbiology · doi:10.1111/j.1462-2920.2009.01913.x · Cited by 63
Search for Bacillus anthracis Potential Vaccine Candidates by a Functional Genomic-Serologic Screen
Gat, O., Grosfeld, H., Ariel, N., Inbar, I., Zaide, G., Broder, Y. C., Zvi, A., Chitlaru, T., Altboum, Z., Stein, D., et al. (2006) · Infection and Immunity · doi:10.1128/iai.00174-06 · Cited by 63
Chapter 1 Enzymatic Formation of Anandamide
Okamoto, Y., Tsuboi, K., & Ueda, N. (2009) · Vitamins and hormones · doi:10.1016/s0083-6729(09)81001-7 · Cited by 62
Lrat-specific domain facilitates Vitamin A metabolism by domain swapping in HRASLS3
Golczak, M., Sears, A. E., Kiser, P. D., & Palczewski, K. (2015) · Nature Chemical Biology · doi:10.1038/nchembio.1687 · Cited by 58
Highly regulated, diversifying NTP-dependent biological conflict systems with implications for the emergence of multicellularity
Kaur, G., Burroughs, A. M., Iyer, L. M., & Aravind, L. (2020) · eLife · doi:10.7554/elife.52696 · Cited by 58
Self-citation
One for All or All for One: Heterogeneous Expression and Host Cell Lysis Are Key to Gene Transfer Agent Activity in Rhodobacter capsulatus
Fogg, P. C. M., Westbye, A. B., & Beatty, J. T. (2012) · PLoS ONE · doi:10.1371/journal.pone.0043772 · Cited by 58
Structure/Function Relationships of Adipose Phospholipase A2 Containing a Cys-His-His Catalytic Triad
Pang, X.-Y., Cao, J., Addington, L., Lovell, S., Battaile, K. P., Zhang, N., Rao, J. L. U. M., Dennis, E. A., & Moise, A. R. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.398859 · Cited by 57
Enzymological analysis of the tumor suppressor A-C1 reveals a novel group of phospholipid-metabolizing enzymes
Shinohara, N., Uyama, T., Jin, X.-H., Tsuboi, K., Tonai, T., Houchi, H., & Ueda, N. (2011) · Journal of Lipid Research · doi:10.1194/jlr.m015081 · Cited by 56
One fold, many functions—M23 family of peptidoglycan hydrolases
Razew, A., Schwarz, J., Mitkowski, P., Sabała, I., & Kaus‐Drobek, M. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.1036964 · Cited by 57
Francisella tularensis IglG Belongs to a Novel Family of PAAR-Like T6SS Proteins and Harbors a Unique N-terminal Extension Required for Virulence
Mélanie, R., Bröms, J. E., Mosnier, A., Hologne, M., Martin, A., Lena, L., Claire, P., Lays, C., Walker, O., Charbit, A., et al. (2016) · PLoS Pathogens · doi:10.1371/journal.ppat.1005821 · Cited by 62
RIG1 suppresses Ras activation and induces cellular apoptosis at the Golgi apparatus
Tsai, F., Shyu, R., & Jiang, S. (2006) · Cellular Signalling · doi:10.1016/j.cellsig.2006.11.005 · Cited by 54
Peptidoglycan Amidase MepA Is a LAS Metallopeptidase
Marcyjaniak, M., Odintsov, S. G., Sabała, I., & Bochtler, M. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m406735200 · Cited by 51
Evolution of Retinoid and Steroid Signaling: Vertebrate Diversification from an Amphioxus Perspective
Albalat, R., Brunet, F., Laudet, V., & Schubert, M. (2011) · Genome Biology and Evolution · doi:10.1093/gbe/evr084 · Cited by 51
RARRES1 expression is significantly related to tumour differentiation and staging in colorectal adenocarcinoma
Wu, C., Shyu, R., Chou, J.-M., Jao, S., Chao, P., Kang, J., Wu, S., Huang, S.-L., & Jiang, S. (2006) · European Journal of Cancer · doi:10.1016/j.ejca.2005.11.015 · Cited by 51
Retinyl esters form lipid droplets independently of triacylglycerol and seipin
Molenaar, M. R., Yadav, K. K., Toulmay, A., Wassenaar, T. A., Mari, M. C., Caillon, L., Chorlay, A., Lukmantara, I., Haaker, M. W., Wubbolts, R., et al. (2021) · The Journal of Cell Biology · doi:10.1083/jcb.202011071 · Cited by 50
RIG1 inhibits the Ras/mitogen-activated protein kinase pathway by suppressing the activation of Ras
Tsai, F., Shyu, R., & Jiang, S. (2005) · Cellular Signalling · doi:10.1016/j.cellsig.2005.05.005 · Cited by 50

Authors: Anantharaman, V., & Aravind, L.
Affiliations: National Institutes of Health (US)
Corresponding author: Aravind, L
ORCID: Anantharaman, Vivek
Aravind, L
Venue: Genome Biology
Publisher: Springer Science and Business Media LLC
Published: 2003-02-03
Volume: 4
Issue: 2
Pages: R11-R11
ISSN: 1465-6906 (ISSN-L)
1474-760X
DOI: 10.1186/gb-2003-4-2-r11
PMC: PMC151301
OpenAlex: W2113183492
Cited by: 365
References: 73
Citations by year: 2026: 9 · 2025: 13 · 2024: 16 · 2023: 13 · 2022: 18 · 2021: 12 · 2020: 21 · 2019: 12 · 2018: 11 · 2017: 9 · 2016: 15 · 2015: 23 · 2014: 17 · 2013: 20 · 2012: 31
FWCI: 7.60
Type: journal article
Language: en
Open access: gold
doi.org
Licence: www.springernature.com/gp/researchers/text-and-data-mining (tdm)
www.springernature.com/gp/researchers/text-and-data-mining (vor)
Locations: Genome biology (publishedVersion)
Europe PMC (PubMed Central) (publishedVersion, other-oa)
PubMed Central (publishedVersion, other-oa)
PubMed (publishedVersion)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biochemical and Structural Characterization
Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
Keywords: peptidoglycan hydrolase, circular permutation, conserved catalytic residues, catalytic triad, acyl transfer, amide hydrolysis, LRAT, domain architecture
MeSH terms: Amino Acid Sequence, Bacterial Proteins, Multigene Family, Models, Molecular, Molecular Sequence Data, Peptide Hydrolases, Phylogeny, Sequence Alignment, Sequence Homology, Amino Acid, Evolution, Molecular

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Evolutionary history, structural features and biochemical diversity of the NlpC/P60 superfamily of enzymes

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks