|
|
| (One intermediate revision not shown.) |
| Line 3: |
Line 3: |
| | <StructureSection load='1xdu' size='340' side='right'caption='[[1xdu]], [[Resolution|resolution]] 2.70Å' scene=''> | | <StructureSection load='1xdu' size='340' side='right'caption='[[1xdu]], [[Resolution|resolution]] 2.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1xdu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25489 Atcc 25489]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XDU OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1XDU FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1xdu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_purpurascens Streptomyces purpurascens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XDU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XDU FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=SFG:SINEFUNGIN'>SFG</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]] 2.7Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SFG:SINEFUNGIN'>SFG</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1qzz|1qzz]], [[1r00|1r00]], [[1tw3|1tw3]], [[1xds|1xds]]</div></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=1xdu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xdu OCA], [https://pdbe.org/1xdu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xdu RCSB], [https://www.ebi.ac.uk/pdbsum/1xdu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xdu ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rdmb ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1924 ATCC 25489])</td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1xdu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xdu OCA], [http://pdbe.org/1xdu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xdu RCSB], [http://www.ebi.ac.uk/pdbsum/1xdu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xdu ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RDMB_STREF RDMB_STREF]] Involved in the biosynthesis of the anthracycline aclacinomycin which is an aromatic polyketide antibiotic that exhibits high cytotoxicity and is widely applied in the chemotherapy of a variety of cancers. In vivo and in vitro, RdmB catalyzes the removal of the carboxylic group from the C-10 position of 15-demethoxyaclacinomycin T coupled to hydroxylation at the same C-10 position. It could also catalyze the removal of the carboxylic group at the C-10 position of 15-demethoxy-epsilon-rhodomycin coupled to hydroxylation at the same C-10 position to yield rhodomycin B. The reaction catalyzes by RdmB is intriguing, since the enzyme does not use any of the cofactors usually associated with hydroxylases such as flavins and/or metal ions to activate molecular oxygen.<ref>PMID:11004563</ref> <ref>PMID:15548527</ref> | + | [https://www.uniprot.org/uniprot/RDMB_STREF RDMB_STREF] Involved in the biosynthesis of the anthracycline aclacinomycin which is an aromatic polyketide antibiotic that exhibits high cytotoxicity and is widely applied in the chemotherapy of a variety of cancers. In vivo and in vitro, RdmB catalyzes the removal of the carboxylic group from the C-10 position of 15-demethoxyaclacinomycin T coupled to hydroxylation at the same C-10 position. It could also catalyze the removal of the carboxylic group at the C-10 position of 15-demethoxy-epsilon-rhodomycin coupled to hydroxylation at the same C-10 position to yield rhodomycin B. The reaction catalyzes by RdmB is intriguing, since the enzyme does not use any of the cofactors usually associated with hydroxylases such as flavins and/or metal ions to activate molecular oxygen.<ref>PMID:11004563</ref> <ref>PMID:15548527</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| Line 17: |
Line 15: |
| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xd/1xdu_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xd/1xdu_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
| Line 35: |
Line 33: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 25489]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Erola, A]] | + | [[Category: Streptomyces purpurascens]] |
| - | [[Category: Jansson, A]] | + | [[Category: Erola A]] |
| - | [[Category: Koskiniemi, H]] | + | [[Category: Jansson A]] |
| - | [[Category: Mantsala, P]] | + | [[Category: Koskiniemi H]] |
| - | [[Category: Niemi, J]] | + | [[Category: Mantsala P]] |
| - | [[Category: Schneider, G]] | + | [[Category: Niemi J]] |
| - | [[Category: Wang, J]] | + | [[Category: Schneider G]] |
| - | [[Category: Anthracycline]]
| + | [[Category: Wang J]] |
| - | [[Category: Divergent evolution]]
| + | |
| - | [[Category: Hydroxylase]]
| + | |
| - | [[Category: Polyketide antibiotic]]
| + | |
| - | [[Category: S-adenosyl-l-methionine analogue]]
| + | |
| - | [[Category: Sinefungin]]
| + | |
| - | [[Category: Streptomyce]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
RDMB_STREF Involved in the biosynthesis of the anthracycline aclacinomycin which is an aromatic polyketide antibiotic that exhibits high cytotoxicity and is widely applied in the chemotherapy of a variety of cancers. In vivo and in vitro, RdmB catalyzes the removal of the carboxylic group from the C-10 position of 15-demethoxyaclacinomycin T coupled to hydroxylation at the same C-10 position. It could also catalyze the removal of the carboxylic group at the C-10 position of 15-demethoxy-epsilon-rhodomycin coupled to hydroxylation at the same C-10 position to yield rhodomycin B. The reaction catalyzes by RdmB is intriguing, since the enzyme does not use any of the cofactors usually associated with hydroxylases such as flavins and/or metal ions to activate molecular oxygen.[1] [2]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Aclacinomycin 10-hydroxylase is a methyltransferase homologue that catalyzes a S-adenosyl-L-methionine (AdoMet)-dependent hydroxylation of the C-10 carbon atom of 15-demethoxy-epsilon-rhodomycin, a step in the biosynthesis of the polyketide antibiotic beta-rhodomycin. S-Adenosyl-L-homocysteine is an inhibitor of the enzyme, whereas the AdoMet analogue sinefungin can act as cofactor, indicating that a positive charge is required for catalysis. 18O2 experiments show that the hydroxyl group is derived from molecular oxygen. The reaction further requires thiol reagents such as glutathione or dithiothreitol. Incubation of the enzyme with substrate in the absence of reductant leads to the accumulation of an intermediate with a molecular mass consistent with a perhydroxy compound. This intermediate is turned into product upon addition of glutathione. The crystal structure of an abortive enzyme-AdoMet product ternary complex reveals large conformational changes consisting of a domain rotation leading to active site closure upon binding of the anthracycline ligand. The data suggest a mechanism where decarboxylation of the substrate results in the formation of a carbanion intermediate, which is stabilized by resonance through the aromatic ring system of the anthracycline substrate. The delocalization of the electrons is facilitated by the positive charge of the cofactor AdoMet. The activation of oxygen and formation of a hydroxyperoxide intermediate occurs in a manner similar to that observed in flavoenzymes. Aclacinomycin-10-hydroxylase is the first example of a AdoMet-dependent hydroxylation reaction, a novel function for this cofactor. The enzyme lacks methyltransferase activity due to the positioning of the AdoMet methyl group unfavorable for a SN2-type methyl transfer to the substrate.
Aclacinomycin 10-hydroxylase is a novel substrate-assisted hydroxylase requiring S-adenosyl-L-methionine as cofactor.,Jansson A, Koskiniemi H, Erola A, Wang J, Mantsala P, Schneider G, Niemi J J Biol Chem. 2005 Feb 4;280(5):3636-44. Epub 2004 Nov 17. PMID:15548527[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Wang Y, Niemi J, Airas K, Ylihonko K, Hakala J, Mantsala P. Modifications of aclacinomycin T by aclacinomycin methyl esterase (RdmC) and aclacinomycin-10-hydroxylase (RdmB) from Streptomyces purpurascens. Biochim Biophys Acta. 2000 Jul 14;1480(1-2):191-200. PMID:11004563
- ↑ Jansson A, Koskiniemi H, Erola A, Wang J, Mantsala P, Schneider G, Niemi J. Aclacinomycin 10-hydroxylase is a novel substrate-assisted hydroxylase requiring S-adenosyl-L-methionine as cofactor. J Biol Chem. 2005 Feb 4;280(5):3636-44. Epub 2004 Nov 17. PMID:15548527 doi:10.1074/jbc.M412095200
- ↑ Jansson A, Koskiniemi H, Erola A, Wang J, Mantsala P, Schneider G, Niemi J. Aclacinomycin 10-hydroxylase is a novel substrate-assisted hydroxylase requiring S-adenosyl-L-methionine as cofactor. J Biol Chem. 2005 Feb 4;280(5):3636-44. Epub 2004 Nov 17. PMID:15548527 doi:10.1074/jbc.M412095200
|
