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| | ==Residual Dipolar Coupling Refinement of Acireductone Dioxygenase from Klebsiella== | | ==Residual Dipolar Coupling Refinement of Acireductone Dioxygenase from Klebsiella== |
| - | <StructureSection load='1zrr' size='340' side='right'caption='[[1zrr]], [[NMR_Ensembles_of_Models | 17 NMR models]]' scene=''> | + | <StructureSection load='1zrr' size='340' side='right'caption='[[1zrr]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1zrr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_oxytocus_perniciosus"_flugge_1886 "bacillus oxytocus perniciosus" flugge 1886]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1m4o 1m4o]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZRR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZRR FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1zrr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Klebsiella_oxytoca Klebsiella oxytoca]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1m4o 1m4o]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZRR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZRR FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1m4o|1m4o]]</div></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></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=1zrr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zrr OCA], [https://pdbe.org/1zrr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zrr RCSB], [https://www.ebi.ac.uk/pdbsum/1zrr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zrr 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=1zrr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zrr OCA], [https://pdbe.org/1zrr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zrr RCSB], [https://www.ebi.ac.uk/pdbsum/1zrr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zrr ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/MTND_KLEOX MTND_KLEOX]] Catalyzes 2 different reactions between oxygene and the acireductone 1,2-dihydroxy-3-keto-5-methylthiopentene (DHK-MTPene) depending upon the metal bound in the active site. Fe-containing acireductone dioxygenase (Fe-ARD) produces formate and 2-keto-4-methylthiobutyrate (KMTB), the alpha-ketoacid precursor of methionine in the methionine recycle pathway. Ni-containing acireductone dioxygenase (Ni-ARD) produces methylthiopropionate, carbon monoxide and formate, and does not lie on the methionine recycle pathway.<ref>PMID:8407993</ref>
| + | [https://www.uniprot.org/uniprot/MTND_KLEOX MTND_KLEOX] Catalyzes 2 different reactions between oxygene and the acireductone 1,2-dihydroxy-3-keto-5-methylthiopentene (DHK-MTPene) depending upon the metal bound in the active site. Fe-containing acireductone dioxygenase (Fe-ARD) produces formate and 2-keto-4-methylthiobutyrate (KMTB), the alpha-ketoacid precursor of methionine in the methionine recycle pathway. Ni-containing acireductone dioxygenase (Ni-ARD) produces methylthiopropionate, carbon monoxide and formate, and does not lie on the methionine recycle pathway.<ref>PMID:8407993</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus oxytocus perniciosus flugge 1886]] | + | [[Category: Klebsiella oxytoca]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Hoefler, C]] | + | [[Category: Hoefler C]] |
| - | [[Category: Ju, T]] | + | [[Category: Ju T]] |
| - | [[Category: Liang, J]] | + | [[Category: Liang J]] |
| - | [[Category: Pochapsky, S S]] | + | [[Category: Pochapsky SS]] |
| - | [[Category: Pochapsky, T C]] | + | [[Category: Pochapsky TC]] |
| - | [[Category: Beta helix]]
| + | |
| - | [[Category: Cupin]]
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| - | [[Category: Methionine salvage]]
| + | |
| - | [[Category: Nickel]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
Function
MTND_KLEOX Catalyzes 2 different reactions between oxygene and the acireductone 1,2-dihydroxy-3-keto-5-methylthiopentene (DHK-MTPene) depending upon the metal bound in the active site. Fe-containing acireductone dioxygenase (Fe-ARD) produces formate and 2-keto-4-methylthiobutyrate (KMTB), the alpha-ketoacid precursor of methionine in the methionine recycle pathway. Ni-containing acireductone dioxygenase (Ni-ARD) produces methylthiopropionate, carbon monoxide and formate, and does not lie on the methionine recycle pathway.[1]
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
Acireductone dioxygenase (ARD) from Klebsiella ATCC 8724 is a metalloenzyme that is capable of catalyzing different reactions with the same substrates (acireductone and O2) depending upon the metal bound in the active site. A model for the solution structure of the paramagnetic Ni2+-containing ARD has been refined using residual dipolar couplings (RDCs) measured in two media. Additional dihedral restraints based on chemical shift (TALOS) were included in the refinement, and backbone structure in the vicinity of the active site was modeled from a crystallographic structure of the mouse homolog of ARD. The incorporation of residual dipolar couplings into the structural refinement alters the relative orientations of several structural features significantly, and improves local secondary structure determination. Comparisons between the solution structures obtained with and without RDCs are made, and structural similarities and differences between mouse and bacterial enzymes are described. Finally, the biological significance of these differences is considered.
A refined model for the structure of acireductone dioxygenase from Klebsiella ATCC 8724 incorporating residual dipolar couplings.,Pochapsky TC, Pochapsky SS, Ju T, Hoefler C, Liang J J Biomol NMR. 2006 Feb;34(2):117-27. PMID:16518698[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Wray JW, Abeles RH. A bacterial enzyme that catalyzes formation of carbon monoxide. J Biol Chem. 1993 Oct 15;268(29):21466-9. PMID:8407993
- ↑ Pochapsky TC, Pochapsky SS, Ju T, Hoefler C, Liang J. A refined model for the structure of acireductone dioxygenase from Klebsiella ATCC 8724 incorporating residual dipolar couplings. J Biomol NMR. 2006 Feb;34(2):117-27. PMID:16518698 doi:10.1007/s10858-005-5735-8
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