TMRPres2D: high quality visual representation of transmembrane protein models

Spyropoulos, Ioannis C.; Liakopoulos, Theodore D.; Bagos, Pantelis G.; Hamodrakas, Stavros J.

doi:10.1093/bioinformatics/bth358

Cited by 132 publications

(106 citation statements)

References 14 publications

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“…Given the high level of conservation of BacA/UppP, these insights open the door to new avenues of research targeting bacterial cell envelope biosynthesis and cell viability as a strategy for the development of antibacterial therapeutics. ) and the data were used to obtain a 2D structure prediction based on TMRPres2D (Spyropoulos et al, 2004). The putative catalytic residues based on identity are indicated in the second cytoplasmic loop by enlarged residues highlighted in red.…”

Section: Discussionmentioning

confidence: 99%

“…Table 1 illustrates that amongst eight different software programs [TMHMM (Möller et al, 2001), TMpred (Hofmann & Stoffel, 1993), (Pasquier & Hamodrakas, 1999), SOSUI (Hirokawa et al, 1998), SPLIT4.0 (Juretić et al, 2002), HMMTOP (Tusnády & Simon, 1998), MEMSAT2 (Jones et al, 1994) and OCTOPUS (Viklund & Elofsson, 2008)] that predict transmembrane helices, only human DOLPP1 and the E. coli PgpB protein are consistently predicted to have all three motifs residing on the same side of the membrane, whilst only one program (OCTOPUS) predicts this arrangement for YeiU/LpxT. We provide the 2D structure predictions for human DOLPP1 and E. coli PgpB and YeiU/LpxT using MEMSAT2 to predict transmembrane helices, as illustrated by TMRPres2D (Spyropoulos et al, 2004). These structures illustrate the disparity in predicting the entire tripartite motif on one side of the membrane (Fig.…”

Section: Undecaprenyl Pyrophosphate Phosphatases In Bacteriamentioning

confidence: 99%

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Conservation of the PTEN catalytic motif in the bacterial undecaprenyl pyrophosphate phosphatase, BacA/UppP

Bickford

Nick

2013

Microbiology

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Isoprenoid lipid carriers are essential in protein glycosylation and bacterial cell envelope biosynthesis. The enzymes involved in their metabolism (synthases, kinases and phosphatases) are therefore critical to cell viability. In this review, we focus on two broad groups of isoprenoid pyrophosphate phosphatases. One group, containing phosphatidic acid phosphatase motifs, includes the eukaryotic dolichyl pyrophosphate phosphatases and proposed recycling bacterial undecaprenol pyrophosphate phosphatases, PgpB, YbjB and YeiU/LpxT. The second group comprises the bacterial undecaprenol pyrophosphate phosphatase, BacA/UppP, responsible for initial formation of undecaprenyl phosphate, which we predict contains a tyrosine phosphate phosphatase motif resembling that of the tumour suppressor, phosphatase and tensin homologue (PTEN). Based on protein sequence alignments across species and 2D structure predictions, we propose catalytic and lipid recognition motifs unique to BacA/UppP enzymes. The verification of our proposed active-site residues would provide new strategies for the development of substratespecific inhibitors which mimic both the lipid and pyrophosphate moieties, leading to the development of novel antimicrobial agents.

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Section: Discussionmentioning

confidence: 99%

Section: Undecaprenyl Pyrophosphate Phosphatases In Bacteriamentioning

confidence: 99%

Conservation of the PTEN catalytic motif in the bacterial undecaprenyl pyrophosphate phosphatase, BacA/UppP

Bickford

Nick

2013

Microbiology

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“…Graphical representation and editing of the phylogenetic tree was performed using PhyloDraw version 0.82 (39). Transmembrane domains were predicted for Dur proteins and visual models were constructed using TMHMM version 2.0 (40) and TMRPres2D version 0.93 (41). The conserved domains within the predicted amino acid sequences were identified using the PFAM data base (42).…”

Section: Methodsmentioning

confidence: 99%

Histatin 5 Uptake by Candida albicans Utilizes Polyamine Transporters Dur3 and Dur31 Proteins

Kumar

Chadha

Saraswat

et al. 2011

Journal of Biological Chemistry

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Background: Salivary histatin 5 (Hst 5) kills the fungal pathogen Candida albicans upon its internalization. Results: Hst 5 requires C. albicans polyamine transporters Dur3 and Dur31 for its uptake and toxicity. Conclusion: C. albicans Dur polyamine transporters recognize and internalize cationic peptides competitively with spermidine. Significance: Modification of Hsts based upon polyamine structure may improve targeting and fungicidal activity.

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“…The introduction of a PTC via a single-nucleotide base change was previously thought to result in the synthesis of a truncated protein; however, recent research has shown that PTC-carrying transcripts are rapidly degraded via the nonsense-mediated mRNA [Spyropoulos et al, 2004]. Mutated residues are shown in white letters on black background and predicted N-glycosylation sites are boxed.…”

Section: Nonsense Mutationsmentioning

confidence: 99%

Sanfilippo syndrome type C: mutation spectrum in the heparan sulfate acetyl-CoA: α-glucosaminide N-acetyltransferase (HGSNAT) gene

et al. 2009

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Mucopolysaccharidosis (MPS) type IIIC or Sanfilippo syndrome type C is a rare autosomal recessive disorder caused by the deficiency of the lysosomal membrane enzyme, heparan sulfate acetyl-CoA (AcCoA): a-glucosaminide N-acetyltransferase (HGSNAT; EC 2.3.1.78), which catalyzes transmembrane acetylation of the terminal glucosamine residues of heparan sulfate prior to their hydrolysis by a-N-acetylglucosaminidase. Lysosomal storage of undegraded heparan sulfate in the cells of affected patients leads to neuronal death, causing neurodegeneration and severely impaired development accompanied by mild visceral and skeletal abnormalities, including mild dwarfism, coarse facies, and joint stiffness. To date, 50 HGSNAT mutations have been identified in MPS IIIC patients: 40 were previously published and 10 novel mutations are reported here. The mutations span the entire structure of the gene and include 13 splice-site mutations, 11 insertions and deletions, 8 nonsense mutations, and 18 missense mutations (http://chromium.liacs.nl/LOVD2/home.php? select_db 5 HGSNAT). In addition, four polymorphisms result in amino acid changes that do not affect activity of the enzyme. In this work we discuss the spectrum of MPS IIIC mutations, their clinical presentation and distribution within the patient population, and speculate how the mutations may affect the structure and function of HGSNAT. Hum Mutat 30,[918][919][920][921][922][923][924][925]

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TMRPres2D: high quality visual representation of transmembrane protein models

Cited by 132 publications

References 14 publications

Conservation of the PTEN catalytic motif in the bacterial undecaprenyl pyrophosphate phosphatase, BacA/UppP

Conservation of the PTEN catalytic motif in the bacterial undecaprenyl pyrophosphate phosphatase, BacA/UppP

Histatin 5 Uptake by Candida albicans Utilizes Polyamine Transporters Dur3 and Dur31 Proteins

Sanfilippo syndrome type C: mutation spectrum in the heparan sulfate acetyl-CoA: α-glucosaminide N-acetyltransferase (HGSNAT) gene

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