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| | ==Oxygenase component of 3-nitrotoluene dioxygenase from Diaphorobacter sp. strain DS2== | | ==Oxygenase component of 3-nitrotoluene dioxygenase from Diaphorobacter sp. strain DS2== |
| - | <StructureSection load='5xbp' size='340' side='right' caption='[[5xbp]], [[Resolution|resolution]] 2.90Å' scene=''> | + | <StructureSection load='5xbp' size='340' side='right'caption='[[5xbp]], [[Resolution|resolution]] 2.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5xbp]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Diaphorobacter_sp._ds2 Diaphorobacter sp. ds2]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5brc 5brc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XBP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XBP FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5xbp]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Diaphorobacter_sp._DS2 Diaphorobacter sp. DS2]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5brc 5brc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XBP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XBP FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">mntAc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1302548 Diaphorobacter sp. DS2]), mntAd ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1302548 Diaphorobacter sp. DS2])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5xbp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xbp OCA], [http://pdbe.org/5xbp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xbp RCSB], [http://www.ebi.ac.uk/pdbsum/5xbp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xbp ProSAT]</span></td></tr> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5xbp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xbp OCA], [https://pdbe.org/5xbp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xbp RCSB], [https://www.ebi.ac.uk/pdbsum/5xbp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xbp ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/M9PW10_9BURK M9PW10_9BURK] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Diaphorobacter sp. ds2]] | + | [[Category: Diaphorobacter sp. DS2]] |
| - | [[Category: Gurunath, R]] | + | [[Category: Large Structures]] |
| - | [[Category: Kumari, A]] | + | [[Category: Gurunath R]] |
| - | [[Category: Ramaswamy, S]] | + | [[Category: Kumari A]] |
| - | [[Category: Singh, D]] | + | [[Category: Ramaswamy S]] |
| - | [[Category: Iron-sulfur cluster]]
| + | [[Category: Singh D]] |
| - | [[Category: Metal binding protein]]
| + | |
| - | [[Category: Nitroaromatic compounds degrader]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Rieske non-heme oxygenase]]
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| Structural highlights
Function
M9PW10_9BURK
Publication Abstract from PubMed
3-nitrotoluene dioxygenase (3NTDO) from Diaphorobacter sp. strain DS2 catalyses the conversion of 3-nitrotoluene (3NT) into a mixture of 3- and 4-methylcatechols with release of nitrite. We report here, X-ray crystal structures of oxygenase and ferredoxin components of 3NTDO at 2.9 A and 2.4 A, respectively. The residues responsible for nitrite release in 3NTDO were further probed by four single and two double mutations in the catalytic site of alpha-subunit of the dioxygenase. Modification of Val 350 to Phe, Ile 204 to Ala, and Asn258 to Val by site directed mutagenesis resulted in inactive enzymes revealing the importance of these residues in catalysis. Docking studies of meta nitrotoluene to the active site of 3NTDO suggested possible orientations of binding that favor the formation of 3-methylcatechol (3MC) over 4-methylcatechol energetically. The electron transfer pathway from ferredoxin subunit to the active site of the oxygenase subunit is also proposed.
Structural and functional studies of ferredoxin and oxygenase components of 3-nitrotoluene dioxygenase from Diaphorobacter sp. strain DS2.,Kumari A, Singh D, Ramaswamy S, Ramanathan G PLoS One. 2017 Apr 27;12(4):e0176398. doi: 10.1371/journal.pone.0176398., eCollection 2017. PMID:28448625[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Kumari A, Singh D, Ramaswamy S, Ramanathan G. Structural and functional studies of ferredoxin and oxygenase components of 3-nitrotoluene dioxygenase from Diaphorobacter sp. strain DS2. PLoS One. 2017 Apr 27;12(4):e0176398. doi: 10.1371/journal.pone.0176398., eCollection 2017. PMID:28448625 doi:http://dx.doi.org/10.1371/journal.pone.0176398
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