|
|
| (2 intermediate revisions not shown.) |
| Line 1: |
Line 1: |
| | + | |
| | ==Structure of Lactate Oxidase at pH4.5 from AEROCOCCUS VIRIDANS== | | ==Structure of Lactate Oxidase at pH4.5 from AEROCOCCUS VIRIDANS== |
| - | <StructureSection load='2zfa' size='340' side='right' caption='[[2zfa]], [[Resolution|resolution]] 1.81Å' scene=''> | + | <StructureSection load='2zfa' size='340' side='right'caption='[[2zfa]], [[Resolution|resolution]] 1.81Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2zfa]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"gaffkya_homari"_hitchner_and_snieszko_1947 "gaffkya homari" hitchner and snieszko 1947]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZFA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZFA FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2zfa]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aerococcus_viridans Aerococcus viridans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZFA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZFA FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</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]] 1.81Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2nli|2nli]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lactate_2-monooxygenase Lactate 2-monooxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.12.4 1.13.12.4] </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=2zfa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zfa OCA], [https://pdbe.org/2zfa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zfa RCSB], [https://www.ebi.ac.uk/pdbsum/2zfa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zfa 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=2zfa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zfa OCA], [http://pdbe.org/2zfa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zfa RCSB], [http://www.ebi.ac.uk/pdbsum/2zfa PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/LOX_AERVM LOX_AERVM] Catalyzes the oxidation of (S)-lactate (L-lactate) to pyruvate, with a reduction of O2 to H2O2 (Ref.1, PubMed:27302031, PubMed:25423902, PubMed:2818595, PubMed:8589073, PubMed:26260739). Cannot oxidize D-lactate, glycolate, and D,L-2-hydroxybutanoate (PubMed:2818595). May be involved in the utilization of L-lactate as an energy source for growth (By similarity).[UniProtKB:O33655]<ref>PMID:25423902</ref> <ref>PMID:26260739</ref> <ref>PMID:27302031</ref> <ref>PMID:2818595</ref> <ref>PMID:8589073</ref> [UniProtKB:O33655] |
| | == 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/zf/2zfa_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zf/2zfa_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 27: |
Line 29: |
| | </div> | | </div> |
| | <div class="pdbe-citations 2zfa" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 2zfa" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Monooxygenase 3D structures|Monooxygenase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Gaffkya homari hitchner and snieszko 1947]] | + | [[Category: Aerococcus viridans]] |
| - | [[Category: Lactate 2-monooxygenase]] | + | [[Category: Large Structures]] |
| - | [[Category: Balasundaresan, D]] | + | [[Category: Balasundaresan D]] |
| - | [[Category: Furuichi, M]] | + | [[Category: Furuichi M]] |
| - | [[Category: Kaneko, H]] | + | [[Category: Kaneko H]] |
| - | [[Category: Kumar, P K.R]] | + | [[Category: Kumar PKR]] |
| - | [[Category: Minagawa, H]] | + | [[Category: Minagawa H]] |
| - | [[Category: Mizuno, H]] | + | [[Category: Mizuno H]] |
| - | [[Category: Suzuki, N]] | + | [[Category: Suzuki N]] |
| - | [[Category: Waga, I]] | + | [[Category: Waga I]] |
| - | [[Category: Yoshida, Y]] | + | [[Category: Yoshida Y]] |
| - | [[Category: D-lactate]]
| + | |
| - | [[Category: Flavoenzyme]]
| + | |
| - | [[Category: Flavoprotein]]
| + | |
| - | [[Category: Fmn]]
| + | |
| - | [[Category: L-lactate oxidase]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
Function
LOX_AERVM Catalyzes the oxidation of (S)-lactate (L-lactate) to pyruvate, with a reduction of O2 to H2O2 (Ref.1, PubMed:27302031, PubMed:25423902, PubMed:2818595, PubMed:8589073, PubMed:26260739). Cannot oxidize D-lactate, glycolate, and D,L-2-hydroxybutanoate (PubMed:2818595). May be involved in the utilization of L-lactate as an energy source for growth (By similarity).[UniProtKB:O33655][1] [2] [3] [4] [5] [UniProtKB:O33655]
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
L-Lactate oxidase (LOX) belongs to a family of flavin mononucleotide (FMN)-dependent alpha-hydroxy acid-oxidizing enzymes. Previously, the crystal structure of LOX (pH 8.0) from Aerococcus viridans was solved, revealing that the active site residues are located around the FMN. Here, we solved the crystal structures of the same enzyme at pH 4.5 and its complex with d-lactate at pH 4.5, in an attempt to analyze the intermediate steps. In the complex structure, the D-lactate resides in the substrate-binding site, but interestingly, an active site base, His265, flips far away from the D-lactate, as compared with its conformation in the unbound state at pH 8.0. This movement probably results from the protonation of His265 during the crystallization at pH 4.5, because the same flip is observed in the structure of the unbound state at pH 4.5. Thus, the present structure appears to mimic an intermediate after His265 abstracts a proton from the substrate. The flip of His265 triggers a large structural rearrangement, creating a new hydrogen bonding network between His265-Asp174-Lys221 and, furthermore, brings molecular oxygen in between D-lactate and His265. This mimic of the ternary complex intermediate enzyme-substrate-O(2) could explain the reductive half-reaction mechanism to release pyruvate through hydride transfer. In the mechanism of the subsequent oxidative half-reaction, His265 flips back, pushing molecular oxygen into the substrate-binding site as the second substrate, and the reverse reaction takes place to produce hydrogen peroxide. During the reaction, the flip-flop action of His265 has a dual role as an active base/acid to define the major chemical steps. Our proposed reaction mechanism appears to be a common mechanistic strategy for this family of enzymes.
X-ray structures of Aerococcus viridans lactate oxidase and its complex with D-lactate at pH 4.5 show an alpha-hydroxyacid oxidation mechanism.,Furuichi M, Suzuki N, Dhakshnamoorhty B, Minagawa H, Yamagishi R, Watanabe Y, Goto Y, Kaneko H, Yoshida Y, Yagi H, Waga I, Kumar PK, Mizuno H J Mol Biol. 2008 Apr 25;378(2):436-46. Epub 2008 Mar 3. PMID:18367206[6]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Stoisser T, Rainer D, Leitgeb S, Wilson DK, Nidetzky B. The Ala -to-Gly substitution in Aerococcus viridans L-lactate oxidase revisited: structural consequences at the catalytic site and effect on reactivity with O and other electron acceptors. FEBS J. 2014 Nov 25. doi: 10.1111/febs.13162. PMID:25423902 doi:http://dx.doi.org/10.1111/febs.13162
- ↑ Stoisser T, Klimacek M, Wilson DK, Nidetzky B. Speeding up the product release: a second-sphere contribution from Tyr191 to the reactivity of L-lactate oxidase revealed in crystallographic and kinetic studies of site-directed variants. FEBS J. 2015 Aug 11. doi: 10.1111/febs.13409. PMID:26260739 doi:http://dx.doi.org/10.1111/febs.13409
- ↑ Stoisser T, Brunsteiner M, Wilson DK, Nidetzky B. Conformational flexibility related to enzyme activity: evidence for a dynamic active-site gatekeeper function of Tyr(215) in Aerococcus viridans lactate oxidase. Sci Rep. 2016 Jun 15;6:27892. doi: 10.1038/srep27892. PMID:27302031 doi:http://dx.doi.org/10.1038/srep27892
- ↑ Duncan JD, Wallis JO, Azari MR. Purification and properties of Aerococcus viridans lactate oxidase. Biochem Biophys Res Commun. 1989 Oct 31;164(2):919-26. PMID:2818595 doi:10.1016/0006-291x(89)91546-5
- ↑ Maeda-Yorita K, Aki K, Sagai H, Misaki H, Massey V. L-lactate oxidase and L-lactate monooxygenase: mechanistic variations on a common structural theme. Biochimie. 1995;77(7-8):631-42. PMID:8589073 doi:10.1016/0300-9084(96)88178-8
- ↑ Furuichi M, Suzuki N, Dhakshnamoorhty B, Minagawa H, Yamagishi R, Watanabe Y, Goto Y, Kaneko H, Yoshida Y, Yagi H, Waga I, Kumar PK, Mizuno H. X-ray structures of Aerococcus viridans lactate oxidase and its complex with D-lactate at pH 4.5 show an alpha-hydroxyacid oxidation mechanism. J Mol Biol. 2008 Apr 25;378(2):436-46. Epub 2008 Mar 3. PMID:18367206 doi:10.1016/j.jmb.2008.02.062
|
