Immunotation of Rv0058
From DrugPedia: A Wikipedia for Drug discovery
(New page: {{immunebox | Name =<b>replicative DNA helicase</b> |image= | width=250 |image2= |Swiss Prot = P71715 | Genbank = 887009 | PDB = 2R5U | DrugBank ...) |
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=General= | =General= | ||
Hexameric DnaB helicase unwinds the DNA double helix during replication of genetic material in bacteria. DnaB is an essential bacterial protein; therefore, it is an important potential target for antibacterial drug discovery.A crystal structure of the N-terminal region of DnaB from the pathogen Mycobacterium tuberculosis (MtDnaBn), determined at 2.0 A resolution have been reported. This structure provides atomic resolution details of formation of the hexameric ring of DnaB by two distinct interfaces. An extensive hydrophobic interface stabilizes a dimer of MtDnaBn by forming a four-helix bundle. The other, less extensive, interface is formed between the dimers, connecting three of them into a hexameric ring. On the basis of crystal packing interactions between MtDnaBn rings,a model of a helicase-primase complex that explains previously observed effects of DnaB mutations on DNA priming have been suggested. | Hexameric DnaB helicase unwinds the DNA double helix during replication of genetic material in bacteria. DnaB is an essential bacterial protein; therefore, it is an important potential target for antibacterial drug discovery.A crystal structure of the N-terminal region of DnaB from the pathogen Mycobacterium tuberculosis (MtDnaBn), determined at 2.0 A resolution have been reported. This structure provides atomic resolution details of formation of the hexameric ring of DnaB by two distinct interfaces. An extensive hydrophobic interface stabilizes a dimer of MtDnaBn by forming a four-helix bundle. The other, less extensive, interface is formed between the dimers, connecting three of them into a hexameric ring. On the basis of crystal packing interactions between MtDnaBn rings,a model of a helicase-primase complex that explains previously observed effects of DnaB mutations on DNA priming have been suggested. | ||
| - | A characterization of the physical interactions between M. tuberculosis DnaA and DnaB using both in vivo methods, such as bacterial | + | A characterization of the physical interactions between M. tuberculosis DnaA and DnaB using both in vivo methods, such as bacterial two hybrid |
| - | assays, and in vitro techniques, such as surface plasmon resonance (SPR) and | + | assays, and in vitro techniques, such as surface plasmon resonance (SPR) and Pull down/Western blotting. The full length |
| - | + | N-terminus (1206 residues) of DnaB was found to interact with DnaA, while the shorter N terminal domain of DnaB (1125 residues), which lacked the linker region, did not. | |
| - | + | ||
==Protein Sequence== | ==Protein Sequence== | ||
>Rv0058, TB.seq 60394:63015 MW:96919 | >Rv0058, TB.seq 60394:63015 MW:96919 | ||
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SAPKKVWAQVRNRLSAKQMMDIQLHEPTMWKHSPSRSRPHRAEARIEDRAIHELARGDAYWDTVVEITSIGDQHVFDGTV | SAPKKVWAQVRNRLSAKQMMDIQLHEPTMWKHSPSRSRPHRAEARIEDRAIHELARGDAYWDTVVEITSIGDQHVFDGTV | ||
SGTHNFVANGISLHNSLEQDADVVILLHRPDAFDRDDPRGGEADFILAKHRNGPTKTVTVAHQLHLSRFANMAR | SGTHNFVANGISLHNSLEQDADVVILLHRPDAFDRDDPRGGEADFILAKHRNGPTKTVTVAHQLHLSRFANMAR | ||
| - | + | * | |
| Line 41: | Line 40: | ||
<td>subject ids</td><td>% identity</td><td>% positives</td><td>alignment length</td><td> evalue</td></tr> | <td>subject ids</td><td>% identity</td><td>% positives</td><td>alignment length</td><td> evalue</td></tr> | ||
| - | <tr><td></td><td> </td><td> </td><td> </td><td> </td></tr> | + | <tr><td>sp|Q9Y230</td><td> 30</td><td> 48</td><td> 91</td><td> 0.33 </td></tr> |
| - | <tr><td></td><td> </td><td> </td><td> </td><td> </td></tr> | + | <tr><td>sp|O43556</td><td> 29</td><td> 43</td><td> 134</td><td> 0.38</td></tr> |
| - | <tr><td></td><td> </td><td> </td><td> </td><td> </td></tr> | + | <tr><td>sp|Q92805</td><td> 38</td><td> 59</td><td> 44</td><td> 0.67</td></tr> |
| - | <tr><td></td><td> </td><td> </td><td> </td><td> </td></tr> | + | <tr><td>sp|O60706</td><td> 43</td><td> 51</td><td> 37</td><td> 2.4 </td></tr> |
| - | <tr><td></td><td> </td><td> </td><td> </td><td> </td></tr></table> | + | <tr><td>sp|P13569</td><td> 35</td><td> 50</td><td> 59</td><td> 3.4 </td></tr></table> |
=Alergen Protein= | =Alergen Protein= | ||
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Link to [http://www.imtech.res.in/raghava/bcepred/bcepred_submission.html Bcepred] | Link to [http://www.imtech.res.in/raghava/bcepred/bcepred_submission.html Bcepred] | ||
<br> | <br> | ||
| - | Result Predicited by []<br> | + | Result Predicited by [http://crdd.osdd.net/drugpedia/images/1321.pdf]<br> |
====ABCpred Analysis==== | ====ABCpred Analysis==== | ||
Link to [http://www.imtech.res.in/raghava/abcpred/ABC_submission.html ABCpred]<br> | Link to [http://www.imtech.res.in/raghava/abcpred/ABC_submission.html ABCpred]<br> | ||
| - | Result Predicited by []<br> | + | Result Predicited by [http://crdd.osdd.net/drugpedia/images/17777777777.pdf]<br> |
====IEDB Analysis==== | ====IEDB Analysis==== | ||
Link to [http://tools.immuneepitope.org/tools/bcell/iedb_input IEDB]<br> | Link to [http://tools.immuneepitope.org/tools/bcell/iedb_input IEDB]<br> | ||
| - | Result Predicited by []<br> | + | Result Predicited by [http://crdd.osdd.net/drugpedia/images/Papi1.pdf]<br> |
=MHC Class-I Binder= | =MHC Class-I Binder= | ||
| Line 83: | Line 82: | ||
Link to [http://www.imtech.res.in/raghava/nhlapred/comp.html nHLApred] | Link to [http://www.imtech.res.in/raghava/nhlapred/comp.html nHLApred] | ||
<br> | <br> | ||
| - | Result Predicited by []<br> | + | Result Predicited by [http://crdd.osdd.net/drugpedia/images/1111111111111.pdf]<br> |
| + | |||
==IEDB Analysis== | ==IEDB Analysis== | ||
Link to [http://tools.immuneepitope.org/analyze/html/mhc_processing.html IEDB] <br> | Link to [http://tools.immuneepitope.org/analyze/html/mhc_processing.html IEDB] <br> | ||
| - | Result Predicted by [] | + | Result Predicted by [http://crdd.osdd.net/drugpedia/images/Amisup1.txt] |
=MHC Class-II Binder= | =MHC Class-II Binder= | ||
==Propred Analysis== | ==Propred Analysis== | ||
Link to [http://www.imtech.res.in/raghava/propred/ Propred]<br> | Link to [http://www.imtech.res.in/raghava/propred/ Propred]<br> | ||
| - | Result Predicted by [] | + | Result Predicted by [http://crdd.osdd.net/drugpedia/images/182.pdf] |
| - | + | ||
==NetMHC-II Analysis== | ==NetMHC-II Analysis== | ||
Link to [http://www.cbs.dtu.dk/services/NetMHCII/ NetMHC-II]<br> | Link to [http://www.cbs.dtu.dk/services/NetMHCII/ NetMHC-II]<br> | ||
| - | Result Predicted by [] | + | Result Predicted by [http://crdd.osdd.net/drugpedia/images/0058.txt] |
=External Links= | =External Links= | ||
Current revision
| Immunotation of Rv0058
| |
| Name | |
| replicative DNA helicase | |
| Identifiers | |
| Swiss Prot | |
| Genbank | |
| PDB | |
| Chemical data | |
| Formula | ? |
| Mol. wt. | 96915.7 Da |
| Pharmacokinetic data | |
| Bioavailability | ? |
| Solubility | ? |
| Isoelectric-Point | 8.81 |
Contents |
[edit] General
Hexameric DnaB helicase unwinds the DNA double helix during replication of genetic material in bacteria. DnaB is an essential bacterial protein; therefore, it is an important potential target for antibacterial drug discovery.A crystal structure of the N-terminal region of DnaB from the pathogen Mycobacterium tuberculosis (MtDnaBn), determined at 2.0 A resolution have been reported. This structure provides atomic resolution details of formation of the hexameric ring of DnaB by two distinct interfaces. An extensive hydrophobic interface stabilizes a dimer of MtDnaBn by forming a four-helix bundle. The other, less extensive, interface is formed between the dimers, connecting three of them into a hexameric ring. On the basis of crystal packing interactions between MtDnaBn rings,a model of a helicase-primase complex that explains previously observed effects of DnaB mutations on DNA priming have been suggested. A characterization of the physical interactions between M. tuberculosis DnaA and DnaB using both in vivo methods, such as bacterial two hybrid assays, and in vitro techniques, such as surface plasmon resonance (SPR) and Pull down/Western blotting. The full length N-terminus (1206 residues) of DnaB was found to interact with DnaA, while the shorter N terminal domain of DnaB (1125 residues), which lacked the linker region, did not.
[edit] Protein Sequence
>Rv0058, TB.seq 60394:63015 MW:96919 MAVVDDLAPGMDSSPPSEDYGRQPPQDLAAEQSVLGGMLLSKDAIADVLERLRPGDFYRPAHQNVYDAILDLYGRGEPAD AVTVAAELDRRGLLRRIGGAPYLHTLISTVPTAANAGYYASIVAEKALLRRLVEAGTRVVQYGYAGAEGADVAEVVDRAQ AEIYDVADRRLSEDFVALEDLLQPTMDEIDAIASSGGLARGVATGFTELDEVTNGLHPGQMVIVAARPGVGKSTLGLDFM RSCSIRHRMASVIFSLEMSKSEIVMRLLSAEAKIKLSDMRSGRMSDDDWTRLARRMSEISEAPLFIDDSPNLTMMEIRAK ARRLRQKANLKLIVVDYLQLMTSGKKYESRQVEVSEFSRHLKLLAKELEVPVVAISQLNRGPEQRTDKKPMLADLRESGC LTASTRILRADTGAEVAFGELMRSGERPMVWSLDERLRMVARPMINVFPSGRKEVFRLRLASGREVEATGSHPFMKFEGW TPLAQLKVGDRIAAPRRVPEPIDTQRMPESELISLARMIGDGSCLKNQPIRYEPVDEANLAAVTVSAAHSDRAAIRDDYL AARVPSLRPARQRLPRGRCTPIAAWLAGLGLFTKRSHEKCVPEAVFRAPNDQVALFLRHLWSAGGSVRWDPTNGQGRVYY GSTSRRLIDDVAQLLLRVGIFSWITHAPKLGGHDSWRLHIHGAKDQVRFLRHVGVHGAEAVAAQEMLRQLKGPVRNPNLD SAPKKVWAQVRNRLSAKQMMDIQLHEPTMWKHSPSRSRPHRAEARIEDRAIHELARGDAYWDTVVEITSIGDQHVFDGTV SGTHNFVANGISLHNSLEQDADVVILLHRPDAFDRDDPRGGEADFILAKHRNGPTKTVTVAHQLHLSRFANMAR
[edit] Human Homologue Blast Result
| subject ids | % identity | % positives | alignment length | evalue |
| sp|Q9Y230 | 30 | 48 | 91 | 0.33 |
| sp|O43556 | 29 | 43 | 134 | 0.38 |
| sp|Q92805 | 38 | 59 | 44 | 0.67 |
| sp|O60706 | 43 | 51 | 37 | 2.4 |
| sp|P13569 | 35 | 50 | 59 | 3.4 |
[edit] Alergen Protein
Link to Algpred
Non Allergen Predicted by AlgPred Server
[edit] Bacterial Toxin Prediction
Link to btxpred
No Hit Fountd by btxpred server.
[edit] Subcellular Location
Link to TBpred
Cyoplasmic
[edit] Antigens
No Hit Found in AntigenDB
No. Hit Found in IEDB
[edit] B cell Epitopes
[edit] BCEpred Analysis
Link to Bcepred
Result Predicited by [1]
[edit] ABCpred Analysis
Link to ABCpred
Result Predicited by [2]
[edit] IEDB Analysis
Link to IEDB
Result Predicited by [3]
[edit] MHC Class-I Binder
[edit] nHLAPred Analysis
Link to nHLApred
Result Predicited by [4]
[edit] IEDB Analysis
Link to IEDB
Result Predicted by [5]
[edit] MHC Class-II Binder
[edit] Propred Analysis
Link to Propred
Result Predicted by [6]
[edit] NetMHC-II Analysis
Link to NetMHC-II
Result Predicted by [7]
[edit] External Links
- Database of Mycobacterium tuberculosis genome sequences and related information.
