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5na1

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NADH:quinone oxidoreductase (NDH-II) from Staphylococcus aureus - holoprotein structure - 2.32 A resolution

Structural highlights

5na1 is a 1 chain structure with sequence from Staphylococcus aureus subsp. aureus NCTC 8325. This structure supersedes the now removed PDB entry 4xdb. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.32Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NDH_STAA8 Alternative, nonproton pumping NADH:quinone oxidoreductase that delivers electrons to the respiratory chain by oxidation of NADH and reduction of quinones, and contributes to the regeneration of NAD(+) (PubMed:26172206, PubMed:28801048). Can use DMN, a menaquinone analog, 2,3-dimethoxy-5,6-dimethyl-benzoquinone (DDB), an ubiquinone analog, or 2,3,5,6-tetramethyl-1,4-benzoquinone (Duroquinone, DQ) a plastoquinone analog as electron acceptors (PubMed:26172206).^[1] ^[2]

Publication Abstract from PubMed

Type II NADH:quinone oxidoreductases (NDH-2s) are membrane bound enzymes that deliver electrons to the respiratory chain by oxidation of NADH and reduction of quinones. In this way, these enzymes also contribute to the regeneration of NAD(+), allowing several metabolic pathways to proceed. As for the other members of the two-Dinucleotide Binding Domains Flavoprotein (tDBDF) superfamily, the enzymatic mechanism of NDH-2s is still little explored and elusive. In this work we addressed the role of the conserved glutamate 172 (E172) residue in the enzymatic mechanism of NDH-2 from Staphylococcus aureus. We aimed to test our earlier hypothesis that E172 plays a key role in proton transfer to allow the protonation of the quinone. For this we performed a complete biochemical characterization of the enzyme's variants E172A, E172Q and E172S. Our steady state kinetic measurements show a clear decrease in the overall reaction rate, and our substrate interaction studies indicate the binding of the two substrates is also affected by these mutations. Interestingly our fast kinetic results show quinone reduction is more affected than NADH oxidation. We have also determined the X-ray crystal structure of the E172S mutant (2.55A) and compared it with the structure of the wild type (2.32A). Together these results support our hypothesis for E172 being of central importance in the catalytic mechanism of NDH-2, which may be extended to other members of the tDBDF superfamily.

The key role of glutamate 172 in the mechanism of type II NADH:quinone oxidoreductase of Staphylococcus aureus.,Sousa FM, Sena FV, Batista AP, Athayde D, Brito JA, Archer M, Oliveira ASF, Soares CM, Catarino T, Pereira MM Biochim Biophys Acta. 2017 Oct;1858(10):823-832. doi:, 10.1016/j.bbabio.2017.08.002. Epub 2017 Aug 8. PMID:28801048^[3]

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

References

↑ Sena FV, Batista AP, Catarino T, Brito JA, Archer M, Viertler M, Madl T, Cabrita EJ, Pereira MM. Type-II NADH:quinone oxidoreductase from Staphylococcus aureus has two distinct binding sites and is rate limited by quinone reduction. Mol Microbiol. 2015 Oct;98(2):272-88. PMID:26172206 doi:10.1111/mmi.13120
↑ Sousa FM, Sena FV, Batista AP, Athayde D, Brito JA, Archer M, Oliveira ASF, Soares CM, Catarino T, Pereira MM. The key role of glutamate 172 in the mechanism of type II NADH:quinone oxidoreductase of Staphylococcus aureus. Biochim Biophys Acta. 2017 Oct;1858(10):823-832. doi:, 10.1016/j.bbabio.2017.08.002. Epub 2017 Aug 8. PMID:28801048 doi:http://dx.doi.org/10.1016/j.bbabio.2017.08.002
↑ Sousa FM, Sena FV, Batista AP, Athayde D, Brito JA, Archer M, Oliveira ASF, Soares CM, Catarino T, Pereira MM. The key role of glutamate 172 in the mechanism of type II NADH:quinone oxidoreductase of Staphylococcus aureus. Biochim Biophys Acta. 2017 Oct;1858(10):823-832. doi:, 10.1016/j.bbabio.2017.08.002. Epub 2017 Aug 8. PMID:28801048 doi:http://dx.doi.org/10.1016/j.bbabio.2017.08.002

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5na1"

@@ Line 1: / Line 1: @@
 ==NADH:quinone oxidoreductase (NDH-II) from Staphylococcus aureus - holoprotein structure - 2.32 A resolution==
-<StructureSection load='5na1' size='340' side='right' caption='[[5na1]], [[Resolution|resolution]] 2.32&Aring;' scene=''>
+<StructureSection load='5na1' size='340' side='right'caption='[[5na1]], [[Resolution|resolution]] 2.32&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5na1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staa8 Staa8]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4xdb 4xdb]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NA1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NA1 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5na1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_NCTC_8325 Staphylococcus aureus subsp. aureus NCTC 8325]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4xdb 4xdb]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NA1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NA1 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.32&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SAOUHSC_00878 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=93061 STAA8])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=5na1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5na1 OCA], [http://pdbe.org/5na1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5na1 RCSB], [http://www.ebi.ac.uk/pdbsum/5na1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5na1 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=5na1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5na1 OCA], [https://pdbe.org/5na1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5na1 RCSB], [https://www.ebi.ac.uk/pdbsum/5na1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5na1 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/NDH_STAA8 NDH_STAA8] Alternative, nonproton pumping NADH:quinone oxidoreductase that delivers electrons to the respiratory chain by oxidation of NADH and reduction of quinones, and contributes to the regeneration of NAD(+) (PubMed:26172206, PubMed:28801048). Can use DMN, a menaquinone analog, 2,3-dimethoxy-5,6-dimethyl-benzoquinone (DDB), an ubiquinone analog, or 2,3,5,6-tetramethyl-1,4-benzoquinone (Duroquinone, DQ) a plastoquinone analog as electron acceptors (PubMed:26172206).<ref>PMID:26172206</ref> <ref>PMID:28801048</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Staa8]]
+[[Category: Large Structures]]
-[[Category: Archer, M]]
+[[Category: Staphylococcus aureus subsp. aureus NCTC 8325]]
-[[Category: Athayde, D]]
+[[Category: Archer M]]
-[[Category: Brito, J A]]
+[[Category: Athayde D]]
-[[Category: Pereira, M M]]
+[[Category: Brito JA]]
-[[Category: Sena, F V]]
+[[Category: Pereira MM]]
-[[Category: Sousa, F M]]
+[[Category: Sena FV]]
-[[Category: Energetic metabolism]]
+[[Category: Sousa FM]]
-[[Category: Nadh]]
-[[Category: Oxidoreductase]]
-[[Category: Respiratory chain]]

5na1

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Current revision

NADH:quinone oxidoreductase (NDH-II) from Staphylococcus aureus - holoprotein structure - 2.32 A resolution

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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