2e77: Difference between revisions

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New page: left|200px<br /><applet load="2e77" size="350" color="white" frame="true" align="right" spinBox="true" caption="2e77, resolution 1.90Å" /> '''Crystal structure of...
 
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[[Image:2e77.jpg|left|200px]]<br /><applet load="2e77" size="350" color="white" frame="true" align="right" spinBox="true"
caption="2e77, resolution 1.90&Aring;" />
'''Crystal structure of L-lactate oxidase with pyruvate complex'''<br />


==Overview==
==Crystal structure of L-lactate oxidase with pyruvate complex==
L-Lactate oxidase (LOX) from Aerococcus viridans catalyzes the oxidation, of L-lactate to pyruvate by the molecular oxygen and belongs to a large, family of 2-hydroxy acid-dependent flavoenzymes. To investigate the, interaction of LOX with pyruvate in structural details and understand the, chemical mechanism of flavin-dependent L-lactate dehydrogenation, the, LOX-pyruvate complex was crystallized and the crystal structure of the, complex has been solved at a resolution of 1.90 Angstrom. One pyruvate, molecule bound to the active site and located near N5 position of FMN for, subunits, A, B, and D in the asymmetric unit, were identified. The, pyruvate molecule is stabilized by the interaction of its carboxylate, group with the side-chain atoms of Tyr40, Arg181, His265, and Arg268, and, of its keto-oxygen atom with the side-chain atoms of Tyr146, Tyr215, and, His265. The alpha-carbon of pyruvate is found to be 3.13 Angstrom from the, N5 atom of FMN at an angle of 105.4 degrees from the flavin N5-N10 axis.
<StructureSection load='2e77' size='340' side='right'caption='[[2e77]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2e77]] is a 4 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=2E77 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E77 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</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=PYR:PYRUVIC+ACID'>PYR</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=2e77 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e77 OCA], [https://pdbe.org/2e77 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e77 RCSB], [https://www.ebi.ac.uk/pdbsum/2e77 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e77 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/e7/2e77_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=2e77 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
L-Lactate oxidase (LOX) from Aerococcus viridans catalyzes the oxidation of L-lactate to pyruvate by the molecular oxygen and belongs to a large family of 2-hydroxy acid-dependent flavoenzymes. To investigate the interaction of LOX with pyruvate in structural details and understand the chemical mechanism of flavin-dependent L-lactate dehydrogenation, the LOX-pyruvate complex was crystallized and the crystal structure of the complex has been solved at a resolution of 1.90 Angstrom. One pyruvate molecule bound to the active site and located near N5 position of FMN for subunits, A, B, and D in the asymmetric unit, were identified. The pyruvate molecule is stabilized by the interaction of its carboxylate group with the side-chain atoms of Tyr40, Arg181, His265, and Arg268, and of its keto-oxygen atom with the side-chain atoms of Tyr146, Tyr215, and His265. The alpha-carbon of pyruvate is found to be 3.13 Angstrom from the N5 atom of FMN at an angle of 105.4 degrees from the flavin N5-N10 axis.


==About this Structure==
Crystallographic study on the interaction of L-lactate oxidase with pyruvate at 1.9 Angstrom resolution.,Li SJ, Umena Y, Yorita K, Matsuoka T, Kita A, Fukui K, Morimoto Y Biochem Biophys Res Commun. 2007 Jul 13;358(4):1002-7. Epub 2007 May 11. PMID:17517371<ref>PMID:17517371</ref>
2E77 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Aerococcus_viridans Aerococcus viridans] with <scene name='pdbligand=FMN:'>FMN</scene> and <scene name='pdbligand=PYR:'>PYR</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E77 OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Crystallographic study on the interaction of L-lactate oxidase with pyruvate at 1.9 Angstrom resolution., Li SJ, Umena Y, Yorita K, Matsuoka T, Kita A, Fukui K, Morimoto Y, Biochem Biophys Res Commun. 2007 Jul 13;358(4):1002-7. Epub 2007 May 11. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17517371 17517371]
</div>
<div class="pdbe-citations 2e77" style="background-color:#fffaf0;"></div>
 
==See Also==
*[[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: Morimoto Y]]
[[Category: Morimoto, Y.]]
[[Category: FMN]]
[[Category: PYR]]
[[Category: fmn]]
[[Category: oxidoreductase]]
[[Category: tim barrel]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 11:58:04 2008''

Latest revision as of 11:35, 25 October 2023

Crystal structure of L-lactate oxidase with pyruvate complexCrystal structure of L-lactate oxidase with pyruvate complex

Structural highlights

2e77 is a 4 chain structure with sequence from Aerococcus viridans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.9Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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) from Aerococcus viridans catalyzes the oxidation of L-lactate to pyruvate by the molecular oxygen and belongs to a large family of 2-hydroxy acid-dependent flavoenzymes. To investigate the interaction of LOX with pyruvate in structural details and understand the chemical mechanism of flavin-dependent L-lactate dehydrogenation, the LOX-pyruvate complex was crystallized and the crystal structure of the complex has been solved at a resolution of 1.90 Angstrom. One pyruvate molecule bound to the active site and located near N5 position of FMN for subunits, A, B, and D in the asymmetric unit, were identified. The pyruvate molecule is stabilized by the interaction of its carboxylate group with the side-chain atoms of Tyr40, Arg181, His265, and Arg268, and of its keto-oxygen atom with the side-chain atoms of Tyr146, Tyr215, and His265. The alpha-carbon of pyruvate is found to be 3.13 Angstrom from the N5 atom of FMN at an angle of 105.4 degrees from the flavin N5-N10 axis.

Crystallographic study on the interaction of L-lactate oxidase with pyruvate at 1.9 Angstrom resolution.,Li SJ, Umena Y, Yorita K, Matsuoka T, Kita A, Fukui K, Morimoto Y Biochem Biophys Res Commun. 2007 Jul 13;358(4):1002-7. Epub 2007 May 11. PMID:17517371[6]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ 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
  2. ↑ 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
  3. ↑ 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
  4. ↑ 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
  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
  6. ↑ Li SJ, Umena Y, Yorita K, Matsuoka T, Kita A, Fukui K, Morimoto Y. Crystallographic study on the interaction of L-lactate oxidase with pyruvate at 1.9 Angstrom resolution. Biochem Biophys Res Commun. 2007 Jul 13;358(4):1002-7. Epub 2007 May 11. PMID:17517371 doi:10.1016/j.bbrc.2007.05.021

2e77, resolution 1.90Å

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