Family Search for PF04379 (DUF525)
PF04379.14 hits 10 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.
PA0591 hypothetical protein (NCBI) from Pseudomonas aeruginosa PAO1
Aligns to 18:104 / 126 (69.0%), covers 97.7% of PF04379, 123.2 bits
- Pseudomonas aeruginosa cells attached to a surface display a typical proteome early as 20 minutes of incubation
Crouzet, PloS one 2017 - “...difference in attachment ability compared to PAO1 control ( S8 Table ). 3 of them (PA0591, PA0950 and PA3675) presented an increase in the attachment capacity (ratio 1.5 to 1.6). For the others (PA0180, PA2235, PA2864, PA3160 and PA3435) there is a large decrease in attachment...”
- “...a flavodoxin and PA2864 encoding a protein of unknown function. Interestingly, for 3 mutant strains (PA0591, PA0950 and PA3675) a net increase in the attachment capacity was observed (ratio 1.5 to 1.6). No clear function is attributed to these genes but we can hypothesize that these...”
ApaG / b0050 DUF525 domain-containing protein ApaG from Escherichia coli K-12 substr. MG1655 (see 4 papers)
S0049 hypothetical protein (NCBI ptt file) from Shigella flexneri 2a str. 2457T
b0050 hypothetical protein (NCBI) from Escherichia coli str. K-12 substr. MG1655
c0063 ApaG protein (NCBI ptt file) from Escherichia coli CFT073
Aligns to 17:103 / 125 (69.6%), covers 97.7% of PF04379, 114.9 bits
- A multiplex oligonucleotide ligation-PCR as a complementary tool for subtyping of Salmonella Typhimurium
Wuyts, Applied microbiology and biotechnology 2015 - “...showed variation among 8 DT1 S . Typhimurium isolates (S0031, S0032, S0036, S0041, S0042, S0043, S0049 and S0050 in Data set S1), which were screened earlier to determine a positive control for the PCR with these markers. For each SNP marker, PCR amplicons were sequenced of...”
- Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K12 through accurate full-length transcripts assembling
Li, BMC genomics 2013 - “...in at least one of our seven samples (Additional file 14 ), and 21 ( b0050, b0137, b1356, b1382, b1419, b1446, b1457, b1607, b1952, b1998, b3471, b3638, b3937, b4325, b4335, b4336, b4593, b4596, b4610, b4615 and b4620 ) of them were expressed in all the seven...”
- Microarray analysis of orthologous genes: conservation of the translational machinery across species at the sequence and expression level
Jiménez, Genome biology 2003 - “...isomerase rRNA modification and chaperone b0049 Yes* COG0639 T Diadenosine tetraphosphatase rRNA modification and chaperone b0050 No COG2967 P Uncharacterized protein affecting Mg 2+ /Co 2+ transport rRNA modification and chaperone b0051 Yes** COG0030 J 6-m-2-A methyltransferase; put. 16S rRNA methyltransferase rRNA modification and chaperone b0052...”
- A functional update of the Escherichia coli K-12 genome
Serres, Genome biology 2001 - “...solvent tolerance b0201 rrsH n 16S rRNA b0001 ec_G0001 thrL l thr operon leader peptide b0050 ec_0078 apaG o Conserved protein b0081 ec_0123 mraZ o Conserved hypothetical protein b0005 ec_G0005 yaaX o Unknown CDS * Gene product type: c, carrier; e, enzyme; f, factor; h, extrachromosomal...”
- Combined, functional genomic-biochemical approach to intermediary metabolism: interaction of acivicin, a glutamine amidotransferase inhibitor, with Escherichia coli K-12
Smulski, Journal of bacteriology 2001 - “...fimA fis fixX flgD b3256 b4015 b4016 b1623 b0111 b0050 b0564 b0469 b0908 b2601 b1704 b3433 b0930 b1597 b3734 b3731 b3732 b3736 b3572 b0778 b1270 b1661 b2155...”
- In vitro and in vivo antibacterial activities of OPC-20011, a novel parenteral broad-spectrum 2-oxaisocephem antibiotic
Matsumoto, Antimicrobial agents and chemotherapy 1998 (secret)
XP_016873022 F-box only protein 3 isoform X4 from Homo sapiens
Aligns to 132:222 / 309 (29.4%), covers 97.7% of PF04379, 102.1 bits
- Crystal structure and interaction studies of the human FBxo3 ApaG domain.
Krzysiak, The FEBS journal 2016 - GeneRIF: we report the X-ray structure of the human FBxo3 ApaG domain, residues 278-407, at 2.0 A resolution
- FBXO3 Protein Promotes Ubiquitylation and Transcriptional Activity of AIRE (Autoimmune Regulator).
Shao, The Journal of biological chemistry 2016 - GeneRIF: AIRE, which is phosphorylated on two specific residues near its N terminus, then binds to the F-box protein 3 (FBXO3) E3 ubiquitin ligase. In turn, this SCF(FBXO3) (SKP1-CUL1-F box) complex ubiquitylates AIRE, increases its binding to the positive transcription elongation factor b (P-TEFb), and potentiates its transcriptional activity.
- F-box protein Fbxo3 targets Smurf1 ubiquitin ligase for ubiquitination and degradation.
Li, Biochemical and biophysical research communications 2015 (PubMed)- GeneRIF: Fbxo3 promotes the proteasomal degradation of Smurf1. Fbxo3 promotes the poly-ubiquitination of Smurf1.
- Virulence factor NSs of rift valley fever virus recruits the F-box protein FBXO3 to degrade subunit p62 of general transcription factor TFIIH.
Kainulainen, Journal of virology 2014 - GeneRIF: Virulence factor NSs of rift valley fever virus recruits the FBXO3 to degrade subunit p62 of general transcription factor TFIIH.
- A combinatorial F box protein directed pathway controls TRAF adaptor stability to regulate inflammation.
Chen, Nature immunology 2013 - GeneRIF: controls TRAF adaptor stability to regulate inflammation
- PML activates transcription by protecting HIPK2 and p300 from SCFFbx3-mediated degradation.
Shima, Molecular and cellular biology 2008 - GeneRIF: Fbx3 formed SCF(Fbx3) ubiquitin ligase and promoted the degradation of HIPK2 and p300 by the ubiquitin-proteasome pathway
- Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Rose, Molecular medicine (Cambridge, Mass.) - GeneRIF: Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
FBX3_HUMAN / Q9UK99 F-box only protein 3 from Homo sapiens (Human) (see paper)
Aligns to 294:384 / 471 (19.3%), covers 97.7% of PF04379, 101.3 bits
- function: Substrate recognition component of the SCF (SKP1-CUL1-F- box protein)-type E3 ubiquitin ligase complex. Mediates the ubiquitination of HIPK2 and probably that of EP300, leading to rapid degradation by the proteasome. In the presence of PML, HIPK2 ubiquitination still occurs, but degradation is prevented. PML, HIPK2 and FBXO3 may act synergically to activate p53/TP53- dependent transactivation.
subunit: Part of a SCF (SKP1-cullin-F-box) protein ligase complex consisting of FBXO3, SKP1, CUL1 and RBX1. Interacts with PML, interaction is direct and takes place either alone or within the SCF complex.
XP_006234719 F-box only protein 3 isoform X2 from Rattus norvegicus
Aligns to 294:384 / 417 (21.8%), covers 97.7% of PF04379, 99.8 bits
NP_997598 F-box only protein 3 isoform 1 from Mus musculus
Aligns to 294:384 / 480 (19.0%), covers 97.7% of PF04379, 99.5 bits
NP_080665 polymerase delta-interacting protein 2 from Mus musculus
Aligns to 252:338 / 368 (23.6%), covers 95.4% of PF04379, 93.4 bits
- Poldip2 is an oxygen-sensitive protein that controls PDH and αKGDH lipoylation and activation to support metabolic adaptation in hypoxia and cancer.
Paredes, Proceedings of the National Academy of Sciences of the United States of America 2018 - GeneRIF: Poldip2 expression is down-regulated by hypoxia in a variety of cell types and basally repressed in triple-negative cancer cells, leading to inhibition of lipoylation of the pyruvate and alpha-KDH complexes and mitochondrial dysfunction.
- Polymerase delta-interacting protein 2 regulates collagen accumulation via activation of the Akt/mTOR pathway in vascular smooth muscle cells.
Fujii, Journal of molecular and cellular cardiology 2016 - GeneRIF: the rate of collagen I degradation was increased in Poldip2(+/-) vs. Poldip2(+/+) MASMs. Conversely, activation of the PI3K/Akt/mTOR signaling pathway, involved in regulation of protein synthesis, was significantly elevated in Poldip2(+/-) MASMs as was beta1-integrin expression.
- Poldip2 knockout results in perinatal lethality, reduced cellular growth and increased autophagy of mouse embryonic fibroblasts.
Brown, PloS one 2014 - GeneRIF: Poldip2 is an essential protein in development, and underline its importance in cell viability and proliferation
- Polymerase δ-interacting protein 2 promotes postischemic neovascularization of the mouse hindlimb.
Amanso, Arteriosclerosis, thrombosis, and vascular biology 2014 - GeneRIF: Suggest Poldip2 promotes ischemia-induced collateral vessel formation via multiple mechanisms that likely involve reactive oxygen species-dependent activation of matrix metalloproteinase activity, as well as enhanced vascular cell growth and survival.
- Polymerase delta interacting protein 2 sustains vascular structure and function.
Sutliff, Arteriosclerosis, thrombosis, and vascular biology 2013 - GeneRIF: Poldip2 expression is necessary for maintainance vascular integrity and function.
- [Study on the novel factors regulating mitochondrial dynamics].
Suenaga, Yakugaku zasshi : Journal of the Pharmaceutical Society of Japan 2010 (PubMed)- GeneRIF: plays a role in the regulation of mitochondrial morphology. (review)
- [DNA polymerase delta-interacting protein 38 is a target gene of microRNA-291a-5p].
Lin, Sheng wu gong cheng xue bao = Chinese journal of biotechnology 2010 (PubMed)- GeneRIF: miR-291a-5p directly inhibited the expression of PDIP38.
- Regulation of mitochondrial morphology and cell survival by Mitogenin I and mitochondrial single-stranded DNA binding protein.
Arakaki, Biochimica et biophysica acta 2006 (PubMed)- GeneRIF: overexpression of Mitogenin I or mitochondrial single-stranded DNA-binding protein increased elongated or fragmented mitochondria in mouse C2C12 myoblast cells, respectively.
NP_001277074 polymerase delta-interacting protein 2 isoform 2 from Homo sapiens
Aligns to 234:320 / 350 (24.9%), covers 95.4% of PF04379, 93.4 bits
- Poldip2 is an oxygen-sensitive protein that controls PDH and αKGDH lipoylation and activation to support metabolic adaptation in hypoxia and cancer.
Paredes, Proceedings of the National Academy of Sciences of the United States of America 2018 - GeneRIF: Increasing mitochondrial lipoylation by forced expression of Poldip2 increases respiration and reduces the growth rate of cancer cells. Study unveils a regulatory mechanism of catabolic enzymes required for metabolic plasticity and highlights the role of Poldip2 as key during hypoxia and cancer cell metabolic adaptation.
- PolDIP2 interacts with human PrimPol and enhances its DNA polymerase activities.
Guilliam, Nucleic acids research 2016 - GeneRIF: findings establish that PolDIP2 can regulate the translesion synthesis polymerase and primer extension activities of PrimPol
- Essential role of POLDIP2 in Tau aggregation and neurotoxicity via autophagy/proteasome inhibition.
Kim, Biochemical and biophysical research communications 2015 (PubMed)- GeneRIF: POLDIP2 plays a crucial role in Tau aggregation via the impairment of autophagy activity, providing insight into Tau aggregation in Tau pathology.
- PDIP38 is translocated to the spliceosomes/nuclear speckles in response to UV-induced DNA damage and is required for UV-induced alternative splicing of MDM2.
Wong, Cell cycle (Georgetown, Tex.) 2013 - GeneRIF: PDIP38 can respond to genotoxic or transcriptional stresses by undergoing translocation to the spliceosomes, where it is a required participant in the regulation of MDM2 alternative splicing.
- DNA polymerase δ-interacting protein 2 is a processivity factor for DNA polymerase λ during 8-oxo-7,8-dihydroguanine bypass.
Maga, Proceedings of the National Academy of Sciences of the United States of America 2013 - GeneRIF: DNA polymerase delta-interacting protein 2 is a processivity factor for DNA polymerase lambda during 8-oxo-7,8-dihydroguanine bypass.
- Complex sense-antisense architecture of TNFAIP1/POLDIP2 on 17q11.2 represents a novel transcriptional structural-functional gene module involved in breast cancer progression.
Grinchuk, BMC genomics 2010 - GeneRIF: suggest that the TNFAIP1/POLDIP2 complex sense-antisense architecture represents a clinically significant transcriptional structural-functional gene module associated with amplification of the genomic region on 17q11.2 in breast cancer.
- Crosstalk between replicative and translesional DNA polymerases: PDIP38 interacts directly with Poleta.
Tissier, DNA repair 2010 (PubMed)- GeneRIF: We demonstrate that PDIP38 (Poldelta interacting protein of 38kDa) directly interacts with the TLS polymerase Poleta. PDIP38 is able to interact directly not only with Poleta but also with the specialized polymerases Rev1 and Polzeta (via Rev7).
- Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
Hendrickson, PloS one 2010 - GeneRIF: Observational study of gene-disease association. (HuGE Navigator)
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PDIP2_HUMAN / Q9Y2S7 Polymerase delta-interacting protein 2; 38 kDa DNA polymerase delta interaction protein; p38 from Homo sapiens (Human) (see paper)
Aligns to 252:338 / 368 (23.6%), covers 95.4% of PF04379, 93.3 bits
- subunit: Interacts with PCNA and POLD2.
SKI16_ARATH / Q9LND7 F-box protein SKIP16; SKP1-interacting partner 16 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
AT1G06110 SKIP16 (SKP1/ASK-interacting protein 16); protein binding (RefSeq) from Arabidopsis thaliana
Aligns to 314:409 / 436 (22.0%), covers 93.1% of PF04379, 87.1 bits
- function: Component of SCF(ASK-cullin-F-box) E3 ubiquitin ligase complexes, which may mediate the ubiquitination and subsequent proteasomal degradation of target proteins.
subunit: Part of a SCF (ASK-cullin-F-box) protein ligase complex (By similarity). Interacts with SKP1A/ASK1, SKP1B/ASK2, ASK4, ASK11 and ASK13. - Evaluation of putative reference genes for gene expression normalization in soybean by quantitative real-time RT-PCR
Hu, BMC molecular biology 2009 - “...Glyma08g05480.1 CK768960 Gma.34482 AT1G58050 Nuclear helicase Unwinding of the DNA double-helix SKIP16 Glyma12g05510.1 CD397253 Gma.6079 AT1G06110 SKP1/Ask-Interacting Protein 16 Protein binding MTP Glyma03g29350.2 CF808703 Gma.7635 AT2G41790 Metalloprotease, Insulin degrading enzyme Protein degradation PEPKR1 Glyma10g38460.1 AW396185 Gma.23799 AT1G12580 Phosphoenolpyruvate Carboxylase-Related Kinase 1 Protein phosphorylation TIP41 Glyma20g26690.1 EV263725...”
- “...( At4G34270 ), HDC ( At1G58050 ) and UKN2 ( At4G33380 ); and SKIP16 ( At1G06110 ), MTP ( At2G41790 ), PEPKR1 ( At1G12580 ) and UKN1 ( At3G13410 ), which were identified as potential reference genes via a soybean microarray gene expression analysis [ 37...”
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory