CDD: NCBI's conserved domain database

Marchler‐Bauer, Aron; Derbyshire, Myra K.; Gonzales, Noreen R.; Lu, Shuo; Chitsaz, Farideh; Geer, Lewis Y.; Geer, Renata C.; He, Jane; Gwadz, Marc; Hurwitz, David I.; Lanczycki, Christopher J.; Lu, Fu; Marchler, Gabriele H.; Song, Jakyoung; Thanki, Narmada; Wang, Zhouxi; Yamashita, Roxanne A.; Zhang, Dachuan; Chen, Zheng; Bryant, Stephen H.

doi:10.1093/nar/gku1221

Cited by 3,005 publications

(2,368 citation statements)

References 13 publications

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“…The putative phosphorylation sight is D55 [12]. Lysine residues are fairly evenly distributed within the protein but are more clustered at the C-terminus, similar to the sequence in CheY from E. coli [13].…”

Section: Resultsmentioning

confidence: 99%

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Post-translational regulation of a Porphyromonas gingivalis regulator

Krishnan

Duncan³

2018

Journal of Oral Microbiology

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Background: Bacteria use two-component signal transduction systems (among others) to perceive and respond to environmental changes. Within the genus Porphyromonas, we observed degeneration of these systems, as exemplified by the loss of RprX, the sensor kinase partner of the RprY.Objective: The purpose of this study was to investigate modulation of RprY function by acetylation.Design: The transcriptional activity of the rprY-pat genes were measured by RT-PCR and 5ʹ-RACE. The acetylation of RprY were detected by western blotting. Electromobility shift and in vitro ChIP assays were used to measure the DNA binding activity of RprY. The expression of RprY target genes was measured by qRT-PCR. Effects of acetylation on phosphorylation of RprY were measured by Phos-tag gels.Results: The rprY gene is cotranscribed with pat. RprY is acetylated in vivo, and autoacetylated in vitro in a reaction that is enhanced by Pat; the CobB sirtuin deacetylates RprY. Acetylation reduced the DNA binding of RprY. Induced oxidative stress decreased production of RprY in vivo, increased its acetylation and increased expression of nqrA.Conclusions: We propose that to compensate for the loss of RprX, P. gingivalis has evolved a novel mechanism to inactivate RprY through acetylation.

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Section: Resultsmentioning

confidence: 99%

“…The protein sequence of Pat is depicted in Figure 3(b) with the conserved domain of the Gcn5-related acetyltransferase (GNAT) family [12] depicted below. These enzymes catalyse the transfer of an acetyl group from acetyl-CoA to the Nε-amino group of a lysine residue in a protein [14].…”

Section: Resultsmentioning

confidence: 99%

Post-translational regulation of a Porphyromonas gingivalis regulator

Krishnan

Duncan³

2018

Journal of Oral Microbiology

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“…2011), NCBI Conserved Domain Database (http://www.ncbi.nlm.nih.gov/cdd/) (Marchler‐Bauer et al. 2015), and UniProt (http://www.uniprot.org/uniprot/). The splice prediction tools used were SpliceSiteFinder‐like (Zhang 1998), MaxEntScan (Yeo and Burge 2004), NNSPLICE (Reese et al.…”

Section: Methodsmentioning

confidence: 99%

Lynch syndrome mutation spectrum in New South Wales, Australia, including 55 novel mutations

Sjursen

McPhillips²,

Scott

et al. 2016

Molec Gen & Gen Med

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BackgroundLynch syndrome, the most frequent hereditary colorectal cancer syndrome, is caused by defects in mismatch repair genes. Genetic testing is important in order to identify mutation carriers who can benefit from intensive surveillance programs. One of the challenges with genetic testing is the interpretation of pathogenicity of detected DNA variants. The aim of this study was to investigate all putative pathogenic variants tested for at the Division of Molecular Medicine, Pathology North, in Newcastle, Australia, to establish whether previous variant classification is in accordance with that recently performed in the InSiGHT collaboration.MethodsPrediction programs and available literature were used to classify new variants or variants without classification.ResultsWe identified 333 mutation positive families, in which 211 different putative pathogenic mismatch repair mutations were found. Most variants with an InSiGHT classification (141 out of 146) were in accordance with our classification. Five variants were discordant, of which one can definitively be reclassified according to the InSiGHT scheme as class 5. Sixty‐four variants had not been classified by InSiGHT, of whom 55 have not been previously reported.ConclusionIn conclusion, we found that our classifications were mostly in accordance with the InSiGHT scheme. In addition to already known MMR mutations, we have also presented 55 novel pathogenic or putative pathogenic mutations.

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“…Multiple sequence alignment and phylogenetic analyses displayed its close relation in plants to soybean predicted zinc‐binding ADH2‐like protein (different from ADH2 studied 27, 28, 29) with 85% sequence similarity (Fig. S2a).…”

Section: Resultsmentioning

confidence: 99%

“…S2A,B). These domains are reportedly involved in various activities such as oxidoreductases, catalysis, and enzymatic reactions providing catalytic and structural stability to the protein 3, 27. Rossmann fold in NAD‐dependent dehydrogenases found in many protein superfamilies (mostly oxidoreductases).…”

Section: Resultsmentioning

confidence: 99%

A novel zinc‐binding alcohol dehydrogenase 2 from Arachis diogoi, expressed in resistance responses against late leaf spot pathogen, induces cell death when transexpressed in tobacco

et al. 2016

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A novel zinc‐binding alcohol dehydrogenase 2 (AdZADH2) was significantly upregulated in a wild peanut, Arachis diogoi treated with conidia of late leaf spot (LLS) pathogen, Phaeoisariopsis personata. This upregulation was not observed in a comparative analysis of cultivated peanut, which is highly susceptible to LLS. This zinc‐binding alcohol dehydrogenase possessed a Rossmann fold containing NADB domain in addition to the MDR domain present in all previously characterized plant ADH genes/proteins. Transient over‐expression of AdZADH2 under an estradiol inducible promoter (XVE) resulted in hypersensitive response (HR)‐like cell death in tobacco leaf. However, the same level of cell death was not observed when the domains were transiently expressed individually. Cell death observed in tobacco was associated with overexpression of cell death related proteins, antioxidative enzymes such as SOD, CAT and APX and pathogenesis‐related (PR) proteins. In A. diogoi, AdZADH2 expression was significantly upregulated in response to the plant signaling hormones salicylic acid, methyl jasmonate, and sodium nitroprusside.

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CDD: NCBI's conserved domain database

Cited by 3,005 publications

References 13 publications

Post-translational regulation of a Porphyromonas gingivalis regulator

Post-translational regulation of a Porphyromonas gingivalis regulator

Lynch syndrome mutation spectrum in New South Wales, Australia, including 55 novel mutations

A novel zinc‐binding alcohol dehydrogenase 2 from Arachis diogoi, expressed in resistance responses against late leaf spot pathogen, induces cell death when transexpressed in tobacco

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