|
|
| (One intermediate revision not shown.) |
| Line 1: |
Line 1: |
| | + | |
| | ==Crystal structure of SnoaB, a cofactor-independent oxygenase from Streptomyces nogalater, determined to 1.9 resolution== | | ==Crystal structure of SnoaB, a cofactor-independent oxygenase from Streptomyces nogalater, determined to 1.9 resolution== |
| - | <StructureSection load='3kng' size='340' side='right' caption='[[3kng]], [[Resolution|resolution]] 1.90Å' scene=''> | + | <StructureSection load='3kng' size='340' side='right'caption='[[3kng]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3kng]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/As_4.1442 As 4.1442]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KNG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KNG FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3kng]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_nogalater Streptomyces nogalater]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KNG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KNG FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.9Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3kg0|3kg0]], [[3kg1|3kg1]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SnoaB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=38314 AS 4.1442])</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=3kng FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kng OCA], [https://pdbe.org/3kng PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kng RCSB], [https://www.ebi.ac.uk/pdbsum/3kng PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kng ProSAT]</span></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=3kng FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kng OCA], [http://pdbe.org/3kng PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3kng RCSB], [http://www.ebi.ac.uk/pdbsum/3kng PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/SNOAB_STRNO SNOAB_STRNO] Involved in the biosynthesis of the anthracycline (aromatic polyketide) antibiotic nogalamycin (PubMed:8760909, PubMed:8668120). Catalyzes the oxygenation of 12-deoxy-nogalonic acid at position 12 to yield nogalonic acid (PubMed:19255477, PubMed:20052967).<ref>PMID:8668120</ref> <ref>PMID:8760909</ref> <ref>PMID:19255477</ref> <ref>PMID:20052967</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kn/3kng_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kn/3kng_consurf.spt"</scriptWhenChecked> |
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| Line 31: |
Line 33: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: As 4 1442]] | + | [[Category: Large Structures]] |
| - | [[Category: Grocholski, T]] | + | [[Category: Streptomyces nogalater]] |
| - | [[Category: Koskiniemi, H]] | + | [[Category: Grocholski T]] |
| - | [[Category: Lindqvist, Y]] | + | [[Category: Koskiniemi H]] |
| - | [[Category: Mantsala, P]] | + | [[Category: Lindqvist Y]] |
| - | [[Category: Niemi, J]] | + | [[Category: Mantsala P]] |
| - | [[Category: Schneider, G]] | + | [[Category: Niemi J]] |
| - | [[Category: Anthracycline]]
| + | [[Category: Schneider G]] |
| - | [[Category: Cofactor-independent]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Oxygenase]]
| + | |
| - | [[Category: Polyketide]]
| + | |
| Structural highlights
Function
SNOAB_STRNO Involved in the biosynthesis of the anthracycline (aromatic polyketide) antibiotic nogalamycin (PubMed:8760909, PubMed:8668120). Catalyzes the oxygenation of 12-deoxy-nogalonic acid at position 12 to yield nogalonic acid (PubMed:19255477, PubMed:20052967).[1] [2] [3] [4]
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
SnoaB is a cofactor-independent monooxygenase that catalyzes the conversion of 12-deoxynogalonic acid to nogalonic acid in the biosynthesis of the aromatic polyketide nogalamycin in Streptomyces nogalater. In vitro (18)O(2) experiments establish that the oxygen atom incorporated into the substrate is derived from molecular oxygen. The crystal structure of the enzyme was determined in two different space groups to 1.7 and 1.9 A resolution, respectively. The enzyme displays the ferredoxin fold, with the characteristic beta-strand exchange at the dimer interface. The crystal structures reveal a putative catalytic triad involving two asparagine residues, Asn18 and Asn63, and a water molecule, which may play important roles in the enzymatic reaction. Site-directed mutagenesis experiments, replacing the two asparagines individually by alanine, led to a 100-fold drop in enzymatic activity. Replacement of an invariant tryptophan residue in the active site of the enzyme by phenylalanine also resulted in an enzyme variant with about 1% residual activity. Taken together, our findings are most consistent with a carbanion mechanism where the deprotonated substrate reacts with molecular oxygen via one electron transfer and formation of a caged radical.
Crystal Structure of the Cofactor-Independent Monooxygenase SnoaB from Streptomyces nogalater: Implications for the Reaction Mechanism.,Grocholski T, Koskiniemi H, Lindqvist Y, Mantsala P, Niemi J, Schneider G Biochemistry. 2010 Jan 12. PMID:20052967[5]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Ylihonko K, Tuikkanen J, Jussila S, Cong L, Mäntsälä P. A gene cluster involved in nogalamycin biosynthesis from Streptomyces nogalater: sequence analysis and complementation of early-block mutations in the anthracycline pathway. Mol Gen Genet. 1996 May 23;251(2):113-20. PMID:8668120 doi:10.1007/BF02172908
- ↑ Ylihonko K, Hakala J, Kunnari T, Mäntsälä P. Production of hybrid anthracycline antibiotics by heterologous expression of Streptomyces nogalater nogalamycin biosynthesis genes. Microbiology (Reading). 1996 Aug;142 ( Pt 8):1965-72. PMID:8760909 doi:10.1099/13500872-142-8-1965
- ↑ Koskiniemi H, Grocholski T, Schneider G, Niemi J. Expression, purification and crystallization of the cofactor-independent monooxygenase SnoaB from the nogalamycin biosynthetic pathway. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Mar 1;65(Pt, 3):256-9. Epub 2009 Feb 14. PMID:19255477 doi:10.1107/S1744309109001389
- ↑ Grocholski T, Koskiniemi H, Lindqvist Y, Mantsala P, Niemi J, Schneider G. Crystal Structure of the Cofactor-Independent Monooxygenase SnoaB from Streptomyces nogalater: Implications for the Reaction Mechanism. Biochemistry. 2010 Jan 12. PMID:20052967 doi:10.1021/bi901985b
- ↑ Grocholski T, Koskiniemi H, Lindqvist Y, Mantsala P, Niemi J, Schneider G. Crystal Structure of the Cofactor-Independent Monooxygenase SnoaB from Streptomyces nogalater: Implications for the Reaction Mechanism. Biochemistry. 2010 Jan 12. PMID:20052967 doi:10.1021/bi901985b
|
