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| | <StructureSection load='6nxi' size='340' side='right'caption='[[6nxi]], [[Resolution|resolution]] 1.61Å' scene=''> | | <StructureSection load='6nxi' size='340' side='right'caption='[[6nxi]], [[Resolution|resolution]] 1.61Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6nxi]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillo_virgola_del_koch"_trevisan_1884 "bacillo virgola del koch" trevisan 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NXI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NXI FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6nxi]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_cholerae Vibrio cholerae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NXI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6NXI 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=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.61Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">apbE, C9J66_08705, EN12_11145, ERS013140_01021, ERS013173_02114, ERS013193_02472, ERS013199_02400, ERS013202_01888 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=666 "Bacillo virgola del Koch" Trevisan 1884])</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=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/FAD:protein_FMN_transferase FAD:protein FMN transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.180 2.7.1.180] </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=6nxi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nxi OCA], [https://pdbe.org/6nxi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6nxi RCSB], [https://www.ebi.ac.uk/pdbsum/6nxi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6nxi 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=6nxi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nxi OCA], [http://pdbe.org/6nxi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nxi RCSB], [http://www.ebi.ac.uk/pdbsum/6nxi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nxi ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/A0A0F4FI39_VIBCL A0A0F4FI39_VIBCL]] Flavin transferase that catalyzes the transfer of the FMN moiety of FAD and its covalent binding to the hydroxyl group of a threonine residue in a target flavoprotein.[RuleBase:RU363002] | + | [https://www.uniprot.org/uniprot/APBE_VIBC3 APBE_VIBC3] Flavin transferase that catalyzes the transfer of the FMN moiety of FAD and its covalent binding to the hydroxyl group of a threonine residue in a target flavoprotein such as NqrB and NqrC, two subunits of the NQR complex. Cannot use directly FMN instead of FAD as substrate.<ref>PMID:23558683</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillo virgola del koch trevisan 1884]] | |
| - | [[Category: FAD:protein FMN transferase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Structural genomic]] | + | [[Category: Vibrio cholerae]] |
| - | [[Category: Chakravarthy, S]] | + | [[Category: Chakravarthy S]] |
| - | [[Category: Fang, X]] | + | [[Category: Fang X]] |
| - | [[Category: Joachimiak, A]] | + | [[Category: Joachimiak A]] |
| - | [[Category: Juarez, O]] | + | [[Category: Juarez O]] |
| - | [[Category: Osipiuk, J]] | + | [[Category: Osipiuk J]] |
| - | [[Category: Apbe]]
| + | |
| - | [[Category: Csgid]]
| + | |
| - | [[Category: Fad]]
| + | |
| - | [[Category: Flavin transferase]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
APBE_VIBC3 Flavin transferase that catalyzes the transfer of the FMN moiety of FAD and its covalent binding to the hydroxyl group of a threonine residue in a target flavoprotein such as NqrB and NqrC, two subunits of the NQR complex. Cannot use directly FMN instead of FAD as substrate.[1]
Publication Abstract from PubMed
The flavin transferase ApbE plays essential roles in bacterial physiology, covalently incorporating FMN cofactors into numerous respiratory enzymes that use the integrated cofactors as electron carriers. In this work we performed a detailed kinetic and structural characterization of Vibrio cholerae WT ApbE and mutants of the conserved residue His-257, to understand its role in substrate binding and in the catalytic mechanism of this family. Bi-substrate kinetic experiments revealed that ApbE follows a random Bi Bi sequential kinetic mechanism, in which a ternary complex is formed, indicating that both substrates must be bound to the enzyme for the reaction to proceed. Steady-state kinetic analyses show that the turnover rates of His-257 mutants are significantly smaller than those of WT ApbE, and have increased Km values for both substrates, indicating that the His-257 residue plays important roles in catalysis and in enzyme-substrate complex formation. Analyses of the pH dependence of ApbE activity indicate that the pKa of the catalytic residue (pK ES1) increases by 2 pH units in the His-257 mutants, suggesting that this residue plays a role in substrate deprotonation. The crystal structures of WT ApbE and an H257G mutant were determined at 1.61 and 1.92 A resolutions, revealing that His-257 is located in the catalytic site and that the substitution does not produce major conformational changes. We propose a reaction mechanism in which His-257 acts as a general base that deprotonates the acceptor residue, which subsequently performs a nucleophilic attack on FAD for flavin transfer.
Conserved residue His-257 of Vibrio cholerae flavin transferase ApbE plays a critical role in substrate binding and catalysis.,Fang X, Osipiuk J, Chakravarthy S, Yuan M, Menzer WM, Nissen D, Liang P, Raba DA, Tuz K, Howard AJ, Joachimiak A, Minh DDL, Juarez O J Biol Chem. 2019 Sep 13;294(37):13800-13810. doi: 10.1074/jbc.RA119.008261. Epub, 2019 Jul 26. PMID:31350338[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Bertsova YV, Fadeeva MS, Kostyrko VA, Serebryakova MV, Baykov AA, Bogachev AV. Alternative pyrimidine biosynthesis protein ApbE is a flavin transferase catalyzing covalent attachment of FMN to a threonine residue in bacterial flavoproteins. J Biol Chem. 2013 May 17;288(20):14276-14286. PMID:23558683 doi:10.1074/jbc.M113.455402
- ↑ Fang X, Osipiuk J, Chakravarthy S, Yuan M, Menzer WM, Nissen D, Liang P, Raba DA, Tuz K, Howard AJ, Joachimiak A, Minh DDL, Juarez O. Conserved residue His-257 of Vibrio cholerae flavin transferase ApbE plays a critical role in substrate binding and catalysis. J Biol Chem. 2019 Sep 13;294(37):13800-13810. doi: 10.1074/jbc.RA119.008261. Epub, 2019 Jul 26. PMID:31350338 doi:http://dx.doi.org/10.1074/jbc.RA119.008261
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