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

Items 101–200 of 367

Novel transglutaminase-like peptidase and C2 domains elucidate the structure, biogenesis and evolution of the ciliary compartment
Zhang, D., & Aravind, L. (2012) · Cell Cycle · doi:10.4161/cc.22068 · Cited by 55
Self-citation
Pathways and disease-causing alterations in visual chromophore production for vertebrate vision
Kiser, P. D., & Palczewski, K. (2020) · Journal of Biological Chemistry · doi:10.1074/jbc.rev120.014405 · Cited by 50
The Genome of the Novel Phage Rtp, with a Rosette-Like Tail Tip, IsHomologous to the Genome of Phage T1
Wietzorrek, A., Schwarz, H., Herrmann, C., & Braun, V. (2006) · Journal of Bacteriology · doi:10.1128/jb.188.4.1419-1436.2006 · Cited by 49
The two-component cell lysis genes holWMY and lysWMY of the Staphylococcus warneri M phage ϕWMY: Cloning, sequencing, expression, and mutational analysis in Escherichia coli
Yokoi, K., Kawahigashi, N., Uchida, M., Sugahara, K., Shinohara, M., Kawasaki, K., Nakamura, S., Taketo, A., & Kodaira, K.-I. (2005) · Gene · doi:10.1016/j.gene.2005.03.006 · Cited by 49
The peptidoglycan hydrolase TcpG is required for efficient conjugative transfer of pCW3 in Clostridium perfringens
Bantwal, R., Bannam, T. L., Porter, C. J., Quinsey, N. S., Lyras, D., Adams, V., & Rood, J. I. (2012) · Plasmid · doi:10.1016/j.plasmid.2011.12.016 · Cited by 48
Structural Insights into the Pseudomonas aeruginosa Type VI Virulence Effector Tse1 Bacteriolysis and Self-protection Mechanisms
Ding, J., Wang, W., Han, F., Zhang, Y., & Wang, D. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.368043 · Cited by 48
Comprehensive Appraisal of the Extracellular Proteins from a Monoderm Bacterium: Theoretical and Empirical Exoproteomes ofListeria monocytogenesEGD-e by Secretomics
Desvaux, M., Dumas, E., Chafsey, I., Chambon, C., & Hébraud, M. (2010) · Journal of Proteome Research · doi:10.1021/pr1003642 · Cited by 47
Lecithin Retinol Acyltransferase Is a Founder Member of a Novel Family of Enzymes
Jahng, W. J., Xue, L., & Rando, R. R. (2003) · Biochemistry · doi:10.1021/bi035370p · Cited by 46
Structural basis for type VI secreted peptidoglycan DL -endopeptidase function, specificity and neutralization inSerratia marcescens
Velupillai, S., English, G., Bui, N. K., Trunk, K., O'Rourke, P. E. F., Rao, V. A., Vollmer, W., Coulthurst, S. J., & Hunter, W. N. (2013) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444913022725 · Cited by 46
Peptidoglycan NlpC/P60 peptidases in bacterial physiology and host interactions
Griffin, M. E., Klupt, S., Espinosa, J., & Hang, H. C. (2022) · Cell chemical biology · doi:10.1016/j.chembiol.2022.11.001 · Cited by 46
Global transcriptional response of Lactobacillus reuteri to the sourdough environment
Hüfner, E., Britton, R. A., Roos, S., Jonsson, H., & Hertel, C. (2008) · Systematic and Applied Microbiology · doi:10.1016/j.syapm.2008.06.005 · Cited by 46
Early Onset Retinal Dystrophy Due to Mutations in LRAT: Molecular Analysis and Detailed Phenotypic Study
Dev Borman, A., Ocaka, L. A., Mackay, D. S., Ripamonti, C., Henderson, R. H., Moradi, P., Hall, G., Black, G. C., Robson, A. G., Holder, G. E., et al. (2012) · Investigative Opthalmology & Visual Science · doi:10.1167/iovs.12-9548 · Cited by 44
Complete genome sequence of a marine roseophage provides evidence into the evolution of gene transfer agents in alphaproteobacteria
Huang, S., Zhang, Y., Chen, F., & Jiao, N. (2011) · Virology Journal · doi:10.1186/1743-422x-8-124 · Cited by 44
P40 and P75 Are Singular Functional Muramidases Present in the Lactobacillus casei /paracasei/rhamnosus Taxon
Bäuerl, C., Abitayeva, G., Sosa-Carrillo, S., Mencher-Beltrán, A., Navarro‐Lleó, N., Coll-Marqués, J. M., Zúñiga, M., Shaikhin, S., & Pérez‐Martínez, G. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.01420 · Cited by 46
Post‐translational control of vegetative cell separation enzymes through a direct interaction with specific inhibitor IseA in Bacillus subtilis
Yamamoto, H., Hashimoto, M., Higashitsuji, Y., Harada, H., Hariyama, N., Takahashi, L., Iwashita, T., Ooiwa, S., & Sekiguchi, J. (2008) · Molecular Microbiology · doi:10.1111/j.1365-2958.2008.06398.x · Cited by 44
Insights into Substrate Specificity of NlpC/P60 Cell Wall Hydrolases Containing Bacterial SH3 Domains
Xu, Q., Mengin‐Lecreulx, D., Liu, X. W., Patin, D., Farr, C. L., Grant, J. C., Chiu, H., Jaroszewski, L., Knuth, M. W., Godzik, A., et al. (2015) · mBio · doi:10.1128/mbio.02327-14 · Cited by 44
Insight into the core and variant exoproteomes of Listeria monocytogenes species by comparative subproteomic analysis
Dumas, E., Desvaux, M., Chambon, C., & Hébraud, M. (2009) · PROTEOMICS · doi:10.1002/pmic.200800765 · Cited by 43
The Bifunctional Cell Wall Hydrolase CwlT Is Needed for Conjugation of the Integrative and Conjugative Element ICEBs1in Bacillus subtilis and B. anthracis
DeWitt, T. A., & Grossman, A. D. (2014) · Journal of Bacteriology · doi:10.1128/jb.00012-14 · Cited by 43
Mechanisms of the HRSL3 tumor suppressor function in ovarian carcinoma cells
Nazarenko, I. A., Schäfer, R., & Sers, C. (2007) · Journal of Cell Science · doi:10.1242/jcs.000018 · Cited by 43
Antibacterial activity produced by Enterococcus spp. isolated from an artisanal Mexican dairy product, Cotija cheese
García‐Cano, I., Serrano-Maldonado, C. E., Olvera-García, M. E., Delgado‐Arciniega, E., Peña-Montes, C., Mendoza‐Hernández, G., & Quirasco, M. (2014) · LWT · doi:10.1016/j.lwt.2014.04.059 · Cited by 41
Conservation of adjacency as evidence of paralogous operons
Janga, S. C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh882 · Cited by 40
Lecithin:Retinol Acyltransferase: A Key Enzyme Involved in the Retinoid (visual) Cycle
Sears, A. E., & Palczewski, K. (2016) · Biochemistry · doi:10.1021/acs.biochem.6b00319 · Cited by 40
Structural Insights into the Effector – Immunity System Tae4/Tai4 from Salmonella typhimurium
Benz, J., Reinstein, J., & Meinhart, A. (2013) · PLoS ONE · doi:10.1371/journal.pone.0067362 · Cited by 40
The structure of the N‐terminal module of the cell wall hydrolase RipA and its role in regulating catalytic activity
Steiner, E. M., Lyngsø, J., Guy, J. E., Bourenkov, G. P., Lindqvist, Y., Schneider, T. R., Pedersen, J. S., Schneider, G., & Schnell, R. (2018) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25523 · Cited by 40
Origin and Evolution of Retinoid Isomerization Machinery in Vertebrate Visual Cycle: Hint from Jawless Vertebrates
Poliakov, E., Gubin, A. N., Stearn, O., Li, Y., Campos, M. M., Gentleman, S., Rogozin, I. B., & Redmond, T. M. (2012) · PLoS ONE · doi:10.1371/journal.pone.0049975 · Cited by 41
An intermolecular binding mechanism involving multiple LysM domains mediates carbohydrate recognition by an endopeptidase
Wong, J. E. M. M., Midtgaard, S. R., Gysel, K., Thygesen, M. B., Sørensen, K. K., Jensen, K. J., Stougaard, J., Thirup, S., & Blaise, M. (2015) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s139900471402793x · Cited by 40
Evolution of the Genetic Machinery of the Visual Cycle: A Novelty of the Vertebrate Eye?
Albalat, R. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr313 · Cited by 40
Streptococcus pyogenes Ser/Thr Kinase-regulated Cell Wall Hydrolase Is a Cell Division Plane-recognizing and Chain-forming Virulence Factor
Pancholi, V., Boël, G., & Jin, H. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.153825 · Cited by 39
Identification of SagA as a novel vaccine target for the prevention of Enterococcus faecium infections
Kropec, A., Sava, I. G., Vonend, C., Sakinc, T., Grohmann, E., & Hüebner, J. (2011) · Microbiology · doi:10.1099/mic.0.053207-0 · Cited by 39
Construction and analysis of a normalized cDNA library fromMetarhizium anisopliaevar.acridumgerminating and differentiating onLocusta migratoriawings
He, M., & Xia, Y. (2008) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.2008.01447.x · Cited by 39
Proteomic and Transcriptomic Analysis of Extracellular Proteins and mRNA Levels inThermobifida fuscaGrown on Cellobiose and Glucose
Chen, S., & Wilson, D. B. (2007) · Journal of Bacteriology · doi:10.1128/jb.00584-07 · Cited by 39
An extraordinary retrotransposon family encoding dual endonucleasesPreprint
Kojima, K. K., & Fujiwara, H. (2005) · Genome Research · doi:10.1101/gr.3271405 · Cited by 39
Identification and classification of papain-like cysteine proteinases
Ozhelvaci, F., & Steczkiewicz, K. (2023) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2023.104801 · Cited by 38
Cooperative binding of LysM domains determines the carbohydrate affinity of a bacterial endopeptidase protein
Wong, J. E. M. M., Alsarraf, H. M. A. B., Kaspersen, J. D., Pedersen, J. S., Stougaard, J., Thirup, S., & Blaise, M. (2013) · FEBS Journal · doi:10.1111/febs.12698 · Cited by 38
Computational analysis of candidate prion-like proteins in bacteria and their role
Iglesias, V., de Groot, N. S., & Ventura, S. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.01123 · Cited by 36
The Ribosomal Protein RPLP0 Mediates PLAAT4-induced Cell Cycle Arrest and Cell Apoptosis
Wang, C., Wang, L., Wu, C., Chen, M., Lee, M., Lin, Y., & Tsai, F. (2019) · Cell Biochemistry and Biophysics · doi:10.1007/s12013-019-00876-3 · Cited by 37
H-rev107 regulates prostaglandin D2 synthase-mediated suppression of cellular invasion in testicular cancer cells
Shyu, R., Wu, C., Wang, C., Tsai, T., Wang, L., Chen, M., Jiang, S., & Tsai, F. (2013) · Journal of Biomedical Science · doi:10.1186/1423-0127-20-30 · Cited by 37
Structural insights into the inhibition of type VI effector Tae3 by its immunity protein Tai3
Cheng, D., Zhang, H., Gao, Z., Wang, W., She, Z., Liu, G., Shen, Y., Su, X., & Dong, Y. (2013) · Biochemical Journal · doi:10.1042/bj20130193 · Cited by 36
Comparative analysis of four Zantedeschia chloroplast genomes: expansion and contraction of the IR region, phylogenetic analyses and SSR genetic diversity assessment
He, S., Yang, Y., Li, Z., Wang, X., Guo, Y., & Wu, H. (2020) · PeerJ · doi:10.7717/peerj.9132 · Cited by 36
Target Genes, Consensus Binding Site, and Role of Phosphorylation for the Response Regulator MtrA ofCorynebacterium glutamicum
Brocker, M., Mack, C., & Bott, M. H. (2010) · Journal of Bacteriology · doi:10.1128/jb.01032-10 · Cited by 36
XadM, a Novel Adhesin of Xanthomonas oryzae pv. oryzae, Exhibits Similarity to Rhs Family Proteins and Is Required for Optimum Attachment, Biofilm Formation, and Virulence
Pradhan, B. B., Ranjan, M., & Chatterjee, S. (2012) · Molecular Plant-Microbe Interactions · doi:10.1094/mpmi-02-12-0049-r · Cited by 36
Cloning and functional characterization of the HRASLS2 gene
Shyu, R.-Y., Hsieh, Y.-H., Tsai, F., Wu, C., & Jiang, S.-Y. (2007) · Amino Acids · doi:10.1007/s00726-007-0612-2 · Cited by 36
Rv2190c, an NlpC/P60 Family Protein, Is Required for Full Virulence of Mycobacterium tuberculosis
Parthasarathy, G., Lun, S., Guo, H., Ammerman, N. C., Geiman, D. E., & Bishai, W. R. (2012) · PLoS ONE · doi:10.1371/journal.pone.0043429 · Cited by 36
LRAT coordinates the negative-feedback regulation of intestinal retinoid biosynthesis from β-carotene
Ramkumar, S., Moon, J., Golczak, M., & von Lintig, J. (2021) · Journal of Lipid Research · doi:10.1016/j.jlr.2021.100055 · Cited by 35
A conserved poxvirus NlpC/P60 superfamily protein contributes to vaccinia virus virulence in mice but not to replication in cell culture
Senkevich, T. G., Wyatt, L. S., Weisberg, A. S., Koonin, E. V., & Moss, B. (2008) · Virology · doi:10.1016/j.virol.2008.01.009 · Cited by 35
Lecithin: retinol acyltransferase protein is distributed in both hepatic stellate cells and endothelial cells of normal rodent and human liver
Nagatsuma, K., Hayashi, Y., Hano, H., Sagara, H., Murakami, K., Saito, M. M., Masaki, T., Lu, T., Tanaka, M., Enzan, H., et al. (2008) · Liver International · doi:10.1111/j.1478-3231.2008.01773.x · Cited by 35
The Rho GTPase inactivation domain in Vibrio cholerae MARTX toxin has a circularly permuted papain-like thiol protease fold
Pei, J.-M., & Grishin, N. V. (2009) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.22447 · Cited by 37
Deletion of cgR_1596 and cgR_2070, Encoding NlpC/P60 Proteins, Causes a Defect in Cell Separation in Corynebacterium glutamicum R
Tsuge, Y., Ogino, H., Teramoto, H., Inui, M., & Yukawa, H. (2008) · Journal of Bacteriology · doi:10.1128/jb.00752-08 · Cited by 35
Rothia from the Human Nose Inhibit Moraxella catarrhalis Colonization with a Secreted Peptidoglycan Endopeptidase
Stubbendieck, R. M., Dissanayake, E., Burnham, P. M., Zelasko, S. E., Temkin, M. I., Wisdorf, S. S., Vrtis, R. F., Gern, J. E., & Currie, C. R. (2023) · mBio · doi:10.1128/mbio.00464-23 · Cited by 33
Bacterial peptidoglycan recycling
Gilmore, M. C., & Cava, F. (2024) · Trends in Microbiology · doi:10.1016/j.tim.2024.11.004 · Cited by 35
Development of a high yielding E. coli periplasmic expression system for the production of humanized Fab' fragments
Ellis, M., Patel, P., Edon, M., Ramage, W., Dickinson, R., & Humphreys, D. P. (2017) · Biotechnology Progress · doi:10.1002/btpr.2393 · Cited by 34
An involvement of phospholipase A/acyltransferase family proteins in peroxisome regulation and plasmalogen metabolism
Uyama, T., Tsuboi, K., & Ueda, N. (2017) · FEBS Letters · doi:10.1002/1873-3468.12787 · Cited by 35
Characterization of Proteins Belonging to the CHAP-Related Superfamily within the Firmicutes
Layec, S., Decaris, B., & Leblond‐Bourget, N. (2007) · Microbial Physiology · doi:10.1159/000106080 · Cited by 34
Id3 is a novel regulator of p27kip1 mRNA in early G1 phase and is required for cell-cycle progression
Chassot, A., Turchi, L., Virolle, T., Fitsialos, G., Batoz, M., Deckert, M., Dulić, V., Meneguzzi, G., Buscà, R., & Ponzio, G. (2007) · Oncogene · doi:10.1038/sj.onc.1210386 · Cited by 34
Induction of apoptosis by the retinoid inducible growth regulator RIG1 depends on the NC motif in HtTA cervical cancer cells
Tsai, F., Shyu, R., Lin, S., Wu, C., & Jiang, S. (2009) · BMC Cell Biology · doi:10.1186/1471-2121-10-15 · Cited by 33
Evidence for activator and repressor functions of the response regulator MtrA fromCorynebacterium glutamicum
Brocker, M., & Bott, M. H. (2006) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.2006.00456.x · Cited by 33
Structural elucidation of the Cys‐His‐Glu‐Asn proteolytic relay in the secreted CHAP domain enzyme from the human pathogen Staphylococcus saprophyticus
Rossi, P., Aramini, J. M., Xiao, R., Chen, C. X., Nwosu, C., Owens, L. A., Maglaqui, M., Nair, R., Fischer, M. J., Acton, T., et al. (2008) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22267 · Cited by 32
A LysM and SH3-Domain Containing Region of the Listeria monocytogenes p60 Protein Stimulates Accessory Cells to Promote Activation of Host NK Cells
Schmidt, R. L., Filak, H. C., Lemon, J. D., Potter, T. A., & Lenz, L. L. (2011) · PLoS Pathogens · doi:10.1371/journal.ppat.1002368 · Cited by 31
Skl, a novel choline‐binding N‐acetylmuramoyl‐ l ‐alanine amidase of Streptococcus mitis SK137 containing a CHAP domain
Llull, D., López, R., & Garcı́a, E. (2006) · FEBS Letters · doi:10.1016/j.febslet.2006.02.060 · Cited by 31
Interaction of the Escherichia coli Lipoprotein NlpI with Periplasmic Prc (Tsp) Protease
Tadokoro, A., Hayashi, H., Kishimoto, T., Makino, Y., Fujisaki, S., & Nishimura, Y. (2004) · The Journal of Biochemistry · doi:10.1093/jb/mvh022 · Cited by 31
The phage shock protein (PSP) envelope stress response: discovery of novel partners and evolutionary history
Ravi, J., Anantharaman, V., Chen, S. Z., Brenner, E. P., Datta, P., Aravind, L., & Gennaro, M. L. (2024) · mSystems · doi:10.1128/msystems.00847-23 · Cited by 31
Self-citation
EC300: a phage-based, bacteriolysin-like protein with enhanced antibacterial activity against Enterococcus faecalis
Proença, D., Leandro, C., García, M., Pimentel, M., & São‐José, C. (2015) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-015-6483-7 · Cited by 30
Identification of Corynebacterium diphtheriae gene involved in adherence to epithelial cells
Kolodkina, V. L., Denisevich, T., & Titov, L. P. (2010) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2010.11.004 · Cited by 30
Expression of the class II tumor suppressor gene RIG1 is directly regulated by p53 tumor suppressor in cancer cell lines
Hsu, T., Chu, C., Jiang, S., Hung, M.-W., Ni, W.-C., Lin, H.-E., & Chang, T. (2012) · FEBS Letters · doi:10.1016/j.febslet.2012.03.020 · Cited by 30
Lipoprotein N -Acylation in Staphylococcus aureus Is Catalyzed by a Two-Component Acyl Transferase System
Gardiner, J. H., Komazin, G., Matsuo, M., Cole, K., Götz, F., & Meredith, T. C. (2020) · mBio · doi:10.1128/mbio.01619-20 · Cited by 29
Novel and Unique Diagnostic Biomarkers forBacillus anthracisInfection
Sela-Abramovich, S., Chitlaru, T., Gat, O., Grosfeld, H., Cohen, O., & Avigdor Shafferman, C. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.00766-09 · Cited by 30
The Origin, Evolution, and Local and Global Dissemination of Antimicrobial Resistance
Aarestrup, F. M. (2019) · ASM Press eBooks · doi:10.1128/9781555817534.ch20 · Cited by 31
Solution structure of the N‐terminal catalytic domain of human H‐REV107 – A novel circular permutated NlpC/P60 domain
Ren, X., Lin, J., Jin, C., & Xia, B. (2010) · FEBS Letters · doi:10.1016/j.febslet.2010.09.015 · Cited by 29
Identification of new Corynebacterium pseudotuberculosis antigens by immunoscreening of gene expression library
Galvão, C. E., Fragoso, S. P., de Oliveira, C. E., Forner, O., Pereira, R. R. B., Soares, C. O., & Rosinha, G. M. S. (2017) · BMC Microbiology · doi:10.1186/s12866-017-1110-7 · Cited by 30
Efficient Biosynthesis of Low-Molecular-Weight Poly-γ-glutamic Acid Based on Stereochemistry Regulation in Bacillus amyloliquefaciens
Sha, Y., Huang, Y., Zhu, Y., Sun, T., Luo, Z., Qiu, Y., Zhan, Y., Lei, P., Li, S., & Xu, H. L. (2020) · ACS Synthetic Biology · doi:10.1021/acssynbio.0c00080 · Cited by 29
TIG3: An Important Regulator of Keratinocyte Proliferation and Survival
Scharadin, T. M., & Eckert, R. L. (2014) · Journal of Investigative Dermatology · doi:10.1038/jid.2014.79 · Cited by 29
Structural and Functional Characterization of an Ancient Bacterial Transglutaminase Sheds Light on the Minimal Requirements for Protein Cross-Linking
Fernandes, C. G., Plácido, D., Lousa, D., Brito, J. A., Isidro, A. L., Soares, C. M., Pohl, J., Carrondo, M. A., Archer, M., & Henriques, A. O. (2015) · Biochemistry · doi:10.1021/acs.biochem.5b00661 · Cited by 29
Drug-like molecules with anti-trypanothione synthetase activity identified by high throughput screening
Benítez, D., Franco, J., Sardi, F., Leyva, A., Durán, R., Choi, G., Yang, G., Kim, T. H., Kim, N., Heo, J., et al. (2022) · Journal of Enzyme Inhibition and Medicinal Chemistry · doi:10.1080/14756366.2022.2045590 · Cited by 28
Cln5 represents a new type of cysteine-based S -depalmitoylase linked to neurodegeneration
Luebben, A. V., Bender, D., Becker, S., Crowther, L. M., Erven, I., Hofmann, K., Söding, J., Klemp, H. G., Bellotti, C., Stäuble, A., et al. (2022) · Science Advances · doi:10.1126/sciadv.abj8633 · Cited by 28
H-REV107-1 Stimulates Growth in Non-Small Cell Lung Carcinomas via the Activation of Mitogenic Signaling
Nazarenko, I. A., Kristiansen, G., Fonfara, S., Fritsche‐Guenther, R., Gieseler, C., Kemmner, W., Schäfer, R., Petersen, I., & Sers, C. (2006) · American Journal Of Pathology · doi:10.2353/ajpath.2006.051341 · Cited by 28
Structures of a Bifunctional Cell Wall Hydrolase CwlT Containing a Novel Bacterial Lysozyme and an NlpC/P60 dl-Endopeptidase
Xu, Q., Chiu, H., Farr, C. L., Jaroszewski, L., Knuth, M. W., Miller, M. D., Lesley, S. A., Godzik, A., Elsliger, M., Deacon, A. M., et al. (2013) · Journal of Molecular Biology · doi:10.1016/j.jmb.2013.09.011 · Cited by 28
Structural Analysis of Papain-Like NlpC/P60 Superfamily Enzymes with a Circularly Permuted Topology Reveals Potential Lipid Binding Sites
Xu, Q., Rawlings, N. D., Chiu, H., Jaroszewski, L., Klock, H. E., Knuth, M. W., Miller, M. D., Elsliger, M., Deacon, A. M., Godzik, A., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0022013 · Cited by 27
Structural biology of 11- cis- retinaldehyde production in the classical visual cycle
Daruwalla, A., Choi, E. H., Palczewski, K., & Kiser, P. D. (2018) · Biochemical Journal · doi:10.1042/bcj20180193 · Cited by 28
Involvement of RARRES3 in the regulation of Wnt proteins acylation and signaling activities in human breast cancer cells
Hsu, T.-H., Jiang, S.-Y., Chan, W.-L., Eckert, R. L., Scharadin, T. M., & Chang, T.-C. (2014) · Cell Death and Differentiation · doi:10.1038/cdd.2014.175 · Cited by 28
An Acyl-covalent Enzyme Intermediate of Lecithin:Retinol Acyltransferase*
Golczak, M., & Palczewski, K. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.152314 · Cited by 27
Involvement of the prostaglandin D2 signal pathway in retinoid-inducible gene 1 (RIG1)-mediated suppression of cell invasion in testis cancer cells
Wu, C., Shyu, R., Wang, C., Tsai, T., Wang, L., Chen, M., Jiang, S., & Tsai, F. (2012) · Biochimica et Biophysica Acta (BBA) - Molecular Cell Research · doi:10.1016/j.bbamcr.2012.08.013 · Cited by 27
Crystal structure of type VI effector Tse1 from Pseudomonas aeruginosa
Zhang, H., Gao, Z., Su, X., & Dong, Y. (2012) · FEBS Letters · doi:10.1016/j.febslet.2012.06.036 · Cited by 27
Genetics of Peptidoglycan Biosynthesis
Pavelka, M. S., Mahapatra, S., & Crick, D. C. (2014) · Microbiology Spectrum · doi:10.1128/microbiolspec.mgm2-0034-2013 · Cited by 27
TIG3 Tumor Suppressor-Dependent Organelle Redistribution and Apoptosis in Skin Cancer Cells
Scharadin, T. M., Jiang, H., Jans, R., Rorke, E. A., & Eckert, R. L. (2011) · PLoS ONE · doi:10.1371/journal.pone.0023230 · Cited by 28
Application of In Vivo Induced Antigen Technology (IVIAT) to Bacillus anthracis
Rollins, S. M., Peppercorn, A., Young, J. S., Drysdale, M., Baresch-Bernal, A., Bikowski, M. V., Ashford, D. A., Quinn, C. P., Handfield, M., Hillman, J. D., et al. (2008) · PLoS ONE · doi:10.1371/journal.pone.0001824 · Cited by 27
Structural insight into how Pseudomonas aeruginosa peptidoglycanhydrolase Tse1 and its immunity protein Tsi1 function
Shang, G., Liu, X., Lu, D., Zhang, J., Li, N., Zhu, C., Liu, S., Yu, Q., Zhao, Y., Zhang, H., et al. (2012) · Biochemical Journal · doi:10.1042/bj20120668 · Cited by 31
A novel peptidoglycan D , L ‐endopeptidase induced by S almonella inside eukaryotic cells contributes to virulence
Rico‐Pérez, G., Pezza, A., Pucciarelli, M. G., de Pedro, M. A., Soncini, F. C., & del Portillo, F. G. (2015) · Molecular Microbiology · doi:10.1111/mmi.13248 · Cited by 30
The RipA and RipB Peptidoglycan Endopeptidases Are Individually Nonessential to Mycobacterium smegmatis
Martinelli, D. J., & Pavelka, M. S. (2016) · Journal of Bacteriology · doi:10.1128/jb.00059-16 · Cited by 26
Evolutionary convergence and divergence in archaeal chromosomal proteins and Chromo-like domains from bacteria and eukaryotes
Kaur, G., Iyer, L. M., Subramanian, S., & Aravind, L. (2018) · Scientific Reports · doi:10.1038/s41598-018-24467-z · Cited by 26
Self-citation
The Protozoan Trichomonas vaginalis Targets Bacteria with Laterally Acquired NlpC/P60 Peptidoglycan Hydrolases
Pinheiro, J., Biboy, J., Vollmer, W., Hirt, R., Keown, J., Artuyants, A., Black, M. M., Goldstone, D., & Simoes-Barbosa, A. (2018) · mBio · doi:10.1128/mbio.01784-18 · Cited by 28
Expression of Mycobacterium tuberculosis NLPC/p60 family protein Rv0024 induce biofilm formation and resistance against cell wall acting anti-tuberculosis drugs in Mycobacterium smegmatis
Padhi, A., Naik, S. K., Sengupta, S., Ganguli, G., & Sonawane, A. (2015) · Microbes and Infection · doi:10.1016/j.micinf.2015.11.007 · Cited by 27
Erratum: Involvement of RARRES3 in the regulation of Wnt proteins acylation and signaling activities in human breast cancer cells
Hsu, T.-H., Jiang, S.-Y., Chang, W.-L., Eckert, R. L., Scharadin, T. M., & Chang, T.-C. (2015) · Cell Death and Differentiation · doi:10.1038/cdd.2015.90 · Cited by 26
Crosslink cleaving enzymes: the smart autolysins that remodel the bacterial cell wall
Rajguru, V., Chatterjee, S., Garde, S., & Reddy, M. (2023) · Trends in Microbiology · doi:10.1016/j.tim.2023.11.004 · Cited by 25
RipD (Rv1566c) from Mycobacterium tuberculosis: adaptation of an NlpC/p60 domain to a non-catalytic peptidoglycan-binding function
Böth, D., Steiner, E. M., Izumi, A., Schneider, G., & Schnell, R. (2013) · Biochemical Journal · doi:10.1042/bj20131227 · Cited by 26
TIG3: a regulator of type I transglutaminase activity in epidermis
Eckert, R. L., Sturniolo, M. T., Jans, R., Kraft, C. A., Jiang, H., & Rorke, E. A. (2008) · Amino Acids · doi:10.1007/s00726-008-0123-9 · Cited by 25
Adhesion properties of toxigenic corynebacteria
Ott, L., & Friedrich-Alexander-Universität Erlangen-Nürnberg, P. F. M. (2018) · AIMS Microbiology · doi:10.3934/microbiol.2018.1.85 · Cited by 25
Substances released from probioticLactobacillus rhamnosusGR-1 potentiate NF-κB activity inEscherichia coli-stimulated urinary bladder cells
Karlsson, M., Scherbak, N. N., Khalaf, H., Olsson, P., & Jaß, J. (2012) · FEMS Immunology & Medical Microbiology · doi:10.1111/j.1574-695x.2012.00994.x · Cited by 25
Crystal Structure of an Uncommon Cellulosome-Related Protein Module from Ruminococcus flavefaciens That Resembles Papain-Like Cysteine Peptidases
Levy-Assaraf, M., Voronov‐Goldman, M., Grinberg, I. R., Weiserman, G., Shimon, L. J. W., Jindou, S., Borovok, I., White, B. A., Bayer, E. A., Lamed, R., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0056138 · Cited by 24
Phospholipase A/Acyltransferase enzyme activity of H-rev107 inhibits the H-RAS signaling pathway
Wang, C., Shyu, R., Wu, C., Tsai, T., Wang, L., Chen, M., Jiang, S., & Tsai, F. (2014) · Journal of Biomedical Science · doi:10.1186/1423-0127-21-36 · Cited by 24
Transcriptomic analysis of human norovirus NS1-2 protein highlights a multifunctional role in murine monocytes
Lateef, Z., Gimenez, G., Baker, E. S., & Ward, V. K. (2017) · BMC Genomics · doi:10.1186/s12864-016-3417-4 · Cited by 23

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