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novPTMenzy: a database for enzymes involved in novel post-translational modifications.

Khater S, Mohanty D - Database (Oxford) (2015)

Bottom Line: Unlike well-known PTMs like phosphorylation, glycosylation, SUMOylation, no bioinformatics resources are available for enzymes associated with novel and unusual PTMs. Therefore, we have developed the novPTMenzy database which catalogs information on the sequence, structure, active site and genomic neighborhood of experimentally characterized enzymes involved in five novel PTMs, namely AMPylation, Eliminylation, Sulfation, Hydroxylation and Deamidation.It also has a specialized analysis interface for some PTMs like AMPylation and Eliminylation.The novPTMenzy database is a unique resource that can aid in discovery of unusual PTM catalyzing enzymes in newly sequenced genomes.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics Centre, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India.

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Related in: MedlinePlus

(A) Results from ‘Search Inhibitory helix’ interface that predicts inter or intra inhibitory helices of Fic domains. Along with classification of the identified inhibitory helix as class I, II or III, it helps in prediction of inhibitory motif. It also shows the structure-based profile–profile alignment based on which the given inhibitory helix was predicted. (B) Screenshot depicting genomic neighborhood of a typical LanL protein containing eliminylation domain. Each gene is represented by a thick black line and the functional domains present in a given gene are depicted by red-colored rectangular boxes with the name of the domain inscribed in the box. novPTMenzy has assigned all functional domains using Pfam database, except for eliminylation domain which has been identified by HMM profiles stored in backend databases of novPTMenzy.
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bav039-F5: (A) Results from ‘Search Inhibitory helix’ interface that predicts inter or intra inhibitory helices of Fic domains. Along with classification of the identified inhibitory helix as class I, II or III, it helps in prediction of inhibitory motif. It also shows the structure-based profile–profile alignment based on which the given inhibitory helix was predicted. (B) Screenshot depicting genomic neighborhood of a typical LanL protein containing eliminylation domain. Each gene is represented by a thick black line and the functional domains present in a given gene are depicted by red-colored rectangular boxes with the name of the domain inscribed in the box. novPTMenzy has assigned all functional domains using Pfam database, except for eliminylation domain which has been identified by HMM profiles stored in backend databases of novPTMenzy.

Mentions: For AMPylation, novPTMenzy provides specific tools for identifying intra or inter inhibitory helices involved in the regulation of AMPylation activity. AMPylation by Fic is known to be regulated by small inhibitory domains present on the same polypeptide chain or on neighboring genes on the genome (21). The inhibitory glutamate in aforementioned helix obstructs the ATP binding site and hence inhibits AMPylation by the Fic domain. Based on the presence of inhibitory helix, Fic proteins are classified as class I, II and III. Class I Fic proteins are regulated by inhibitory helices present in neighboring proteins whereas class II and class III proteins are regulated by inhibitory helices present in N-terminal and C-terminal of the Fic domain, respectively. It was shown that the inhibitory helix contains a conserved motif containing the glutamate. To identify the inhibitory domain either in the Fic protein or in their genomic neighborhood, novPTMenzy uses the structure-based profile–profile comparison tool HHSearch (57). Profile HMMs for all the available Fic/Doc structures were built and stored in the backend database. The additional advantage of HHSearch over other profile-based method is the incorporation of secondary structure information in its profile and use of iterative searches to build them. Also, HHsearch relies on profile–profile comparison rather than sequence–profile comparison. This makes HHSearch more compute intensive but its higher sensitivity allows the detection of short helices with divergent sequence containing the inhibitory glutamate. HHpred profiles were built for class II Fic domain BtFic (PDB ID: 3CUC) and SoFic (PDB ID: 3EQX), class III Fic domains NmFic (2G03) and HpFic (2F6S) and for class I inhibitory protein VbhA (3SHG) present in the genomic neighborhood of VbhT Fic domain. These structure-based sequence profiles were stored in our database along with information about the inhibitory motif. Users have an option of giving either just a Fic protein or Fic protein along with its neighbors (maximum 2). For each input sequence HHPred profiles containing structural information are built. The structural information is based on PSIPRED (58) predicted secondary structure. The profiles corresponding to input Fic proteins are compared with the profiles stored for class II and class III Fic proteins in our database. If the alignment has an e-value of <0.001 it is checked for presence of a helix corresponding to inhibitory helix of class II and class III proteins. If the inhibitory glutamate is present in the helix, the query protein is classified as class II or III Fic by novPTMenzy. If the inhibitory glutamate and helix is not located in the Fic protein, profiles of neighbors are aligned to VbhT profile. The Fic protein is labeled as class I based on the presence of inhibitory glutamate in the profile of the neighbor. An option to input the accession numbers of Fic sequences is also available. Accession numbers are mapped to NCBI accession numbers and the sequences are fetched from a locally downloaded nr database. Also, the sequences of its neighbors are retrieved from completely or partially sequenced genomes. novPTMenzy has stored the genomic positions of all proteins from completely sequenced genomes based on information from NCBI’s Mapviewer. A search for inhibitory glutamate is done as described. Figure 5A shows a typical output for inhibitory helix search, when a Fic protein Huntingtin yeast partner E (HYPE) from Rattus norvegicus is given as input. The best hit using structure-based profile–profile match is 3CUC and HYPE is classified as a Fic domain containing class II inhibitory helix with a motif TVAIEG (Figure 5A). It may be noted that HYPE from Homo sapiens has been experimentally shown to be a Fic domain containing class II inhibitory helix (21). This module of novPTMenzy would help biochemists in designing experiments for detailed study of regulation of Fic domains.Figure 5.


novPTMenzy: a database for enzymes involved in novel post-translational modifications.

Khater S, Mohanty D - Database (Oxford) (2015)

(A) Results from ‘Search Inhibitory helix’ interface that predicts inter or intra inhibitory helices of Fic domains. Along with classification of the identified inhibitory helix as class I, II or III, it helps in prediction of inhibitory motif. It also shows the structure-based profile–profile alignment based on which the given inhibitory helix was predicted. (B) Screenshot depicting genomic neighborhood of a typical LanL protein containing eliminylation domain. Each gene is represented by a thick black line and the functional domains present in a given gene are depicted by red-colored rectangular boxes with the name of the domain inscribed in the box. novPTMenzy has assigned all functional domains using Pfam database, except for eliminylation domain which has been identified by HMM profiles stored in backend databases of novPTMenzy.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4414956&req=5

bav039-F5: (A) Results from ‘Search Inhibitory helix’ interface that predicts inter or intra inhibitory helices of Fic domains. Along with classification of the identified inhibitory helix as class I, II or III, it helps in prediction of inhibitory motif. It also shows the structure-based profile–profile alignment based on which the given inhibitory helix was predicted. (B) Screenshot depicting genomic neighborhood of a typical LanL protein containing eliminylation domain. Each gene is represented by a thick black line and the functional domains present in a given gene are depicted by red-colored rectangular boxes with the name of the domain inscribed in the box. novPTMenzy has assigned all functional domains using Pfam database, except for eliminylation domain which has been identified by HMM profiles stored in backend databases of novPTMenzy.
Mentions: For AMPylation, novPTMenzy provides specific tools for identifying intra or inter inhibitory helices involved in the regulation of AMPylation activity. AMPylation by Fic is known to be regulated by small inhibitory domains present on the same polypeptide chain or on neighboring genes on the genome (21). The inhibitory glutamate in aforementioned helix obstructs the ATP binding site and hence inhibits AMPylation by the Fic domain. Based on the presence of inhibitory helix, Fic proteins are classified as class I, II and III. Class I Fic proteins are regulated by inhibitory helices present in neighboring proteins whereas class II and class III proteins are regulated by inhibitory helices present in N-terminal and C-terminal of the Fic domain, respectively. It was shown that the inhibitory helix contains a conserved motif containing the glutamate. To identify the inhibitory domain either in the Fic protein or in their genomic neighborhood, novPTMenzy uses the structure-based profile–profile comparison tool HHSearch (57). Profile HMMs for all the available Fic/Doc structures were built and stored in the backend database. The additional advantage of HHSearch over other profile-based method is the incorporation of secondary structure information in its profile and use of iterative searches to build them. Also, HHsearch relies on profile–profile comparison rather than sequence–profile comparison. This makes HHSearch more compute intensive but its higher sensitivity allows the detection of short helices with divergent sequence containing the inhibitory glutamate. HHpred profiles were built for class II Fic domain BtFic (PDB ID: 3CUC) and SoFic (PDB ID: 3EQX), class III Fic domains NmFic (2G03) and HpFic (2F6S) and for class I inhibitory protein VbhA (3SHG) present in the genomic neighborhood of VbhT Fic domain. These structure-based sequence profiles were stored in our database along with information about the inhibitory motif. Users have an option of giving either just a Fic protein or Fic protein along with its neighbors (maximum 2). For each input sequence HHPred profiles containing structural information are built. The structural information is based on PSIPRED (58) predicted secondary structure. The profiles corresponding to input Fic proteins are compared with the profiles stored for class II and class III Fic proteins in our database. If the alignment has an e-value of <0.001 it is checked for presence of a helix corresponding to inhibitory helix of class II and class III proteins. If the inhibitory glutamate is present in the helix, the query protein is classified as class II or III Fic by novPTMenzy. If the inhibitory glutamate and helix is not located in the Fic protein, profiles of neighbors are aligned to VbhT profile. The Fic protein is labeled as class I based on the presence of inhibitory glutamate in the profile of the neighbor. An option to input the accession numbers of Fic sequences is also available. Accession numbers are mapped to NCBI accession numbers and the sequences are fetched from a locally downloaded nr database. Also, the sequences of its neighbors are retrieved from completely or partially sequenced genomes. novPTMenzy has stored the genomic positions of all proteins from completely sequenced genomes based on information from NCBI’s Mapviewer. A search for inhibitory glutamate is done as described. Figure 5A shows a typical output for inhibitory helix search, when a Fic protein Huntingtin yeast partner E (HYPE) from Rattus norvegicus is given as input. The best hit using structure-based profile–profile match is 3CUC and HYPE is classified as a Fic domain containing class II inhibitory helix with a motif TVAIEG (Figure 5A). It may be noted that HYPE from Homo sapiens has been experimentally shown to be a Fic domain containing class II inhibitory helix (21). This module of novPTMenzy would help biochemists in designing experiments for detailed study of regulation of Fic domains.Figure 5.

Bottom Line: Unlike well-known PTMs like phosphorylation, glycosylation, SUMOylation, no bioinformatics resources are available for enzymes associated with novel and unusual PTMs. Therefore, we have developed the novPTMenzy database which catalogs information on the sequence, structure, active site and genomic neighborhood of experimentally characterized enzymes involved in five novel PTMs, namely AMPylation, Eliminylation, Sulfation, Hydroxylation and Deamidation.It also has a specialized analysis interface for some PTMs like AMPylation and Eliminylation.The novPTMenzy database is a unique resource that can aid in discovery of unusual PTM catalyzing enzymes in newly sequenced genomes.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics Centre, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India.

Show MeSH
Related in: MedlinePlus