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| - | [[Image:2nli.jpg|left|200px]] | |
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| - | <!-- | + | ==Crystal Structure of the complex between L-lactate oxidase and a substrate analogue at 1.59 angstrom resolution== |
| - | The line below this paragraph, containing "STRUCTURE_2nli", creates the "Structure Box" on the page.
| + | <StructureSection load='2nli' size='340' side='right'caption='[[2nli]], [[Resolution|resolution]] 1.59Å' scene=''> |
| - | You may change the PDB parameter (which sets the PDB file loaded into the applet) | + | == Structural highlights == |
| - | or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| + | <table><tr><td colspan='2'>[[2nli]] 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=2NLI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NLI FirstGlance]. <br> |
| - | or leave the SCENE parameter empty for the default display.
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.59Å</td></tr> |
| - | --> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=LAC:LACTIC+ACID'>LAC</scene>, <scene name='pdbligand=PEO:HYDROGEN+PEROXIDE'>PEO</scene></td></tr> |
| - | {{STRUCTURE_2nli| PDB=2nli | SCENE= }}
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2nli FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nli OCA], [https://pdbe.org/2nli PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nli RCSB], [https://www.ebi.ac.uk/pdbsum/2nli PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nli ProSAT]</span></td></tr> |
| | + | </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 == |
| | + | [[Image:Consurf_key_small.gif|200px|right]] |
| | + | Check<jmol> |
| | + | <jmolCheckbox> |
| | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nl/2nli_consurf.spt"</scriptWhenChecked> |
| | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | + | <text>to colour the structure by Evolutionary Conservation</text> |
| | + | </jmolCheckbox> |
| | + | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2nli ConSurf]. |
| | + | <div style="clear:both"></div> |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == 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. |
| | | | |
| - | '''Crystal Structure of the complex between L-lactate oxidase and a substrate analogue at 1.59 angstrom resolution'''
| + | 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<ref>PMID:18367206</ref> |
| - | | + | |
| - | | + | |
| - | ==Overview==
| + | |
| - | 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.
| + | |
| | | | |
| - | ==About this Structure==
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| - | 2NLI is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Aerococcus_viridans Aerococcus viridans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NLI OCA].
| + | </div> |
| | + | <div class="pdbe-citations 2nli" style="background-color:#fffaf0;"></div> |
| | | | |
| - | ==Reference== | + | ==See Also== |
| - | 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:[http://www.ncbi.nlm.nih.gov/pubmed/18367206 18367206]
| + | *[[Monooxygenase 3D structures|Monooxygenase 3D structures]] |
| | + | == References == |
| | + | <references/> |
| | + | __TOC__ |
| | + | </StructureSection> |
| | [[Category: Aerococcus viridans]] | | [[Category: Aerococcus viridans]] |
| - | [[Category: Lactate 2-monooxygenase]] | + | [[Category: Large Structures]] |
| - | [[Category: Single protein]]
| + | [[Category: Balasundaresan D]] |
| - | [[Category: Balasundaresan, D.]] | + | [[Category: Furuichi M]] |
| - | [[Category: Furuichi, M.]] | + | [[Category: Kaneko H]] |
| - | [[Category: Kaneko, H.]] | + | [[Category: Kumar PKR]] |
| - | [[Category: Kumar, P K.R.]] | + | [[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: Watanabe Y]] |
| - | [[Category: Watanabe, Y.]] | + | [[Category: Yoshida Y]] |
| - | [[Category: Yoshida, Y.]] | + | |
| - | [[Category: D-lactate]]
| + | |
| - | [[Category: Flavoenzyme]]
| + | |
| - | [[Category: Fmn]]
| + | |
| - | [[Category: L-lactate oxidase]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Apr 24 09:25:02 2008''
| + | |
| 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
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