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| | <StructureSection load='6qlv' size='340' side='right'caption='[[6qlv]], [[Resolution|resolution]] 2.39Å' scene=''> | | <StructureSection load='6qlv' size='340' side='right'caption='[[6qlv]], [[Resolution|resolution]] 2.39Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6qlv]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QLV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6QLV FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6qlv]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QLV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6QLV FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=HJN:[(2~{R},3~{S},4~{S})-5-[5-[(2~{Z})-3,7-dimethylocta-2,6-dienyl]-7,8-dimethyl-2,4-bis(oxidanylidene)-1~{H}-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl]+dihydrogen+phosphate'>HJN</scene>, <scene name='pdbligand=HZZ:[(2~{Z})-3,7-dimethylocta-2,6-dienyl]+dihydrogen+phosphate'>HZZ</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2.391Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ubiX, C0044_29760, C8257_05245, CAZ10_26235, CGU42_07325, DT376_15100, DZ940_19110, DZ962_23875, NCTC13719_00955, PAERUG_E15_London_28_01_14_05236, PAMH19_1010, RW109_RW109_01660 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=HJN:[(2~{R},3~{S},4~{S})-5-[5-[(2~{Z})-3,7-dimethylocta-2,6-dienyl]-7,8-dimethyl-2,4-bis(oxidanylidene)-1~{H}-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl]+dihydrogen+phosphate'>HJN</scene>, <scene name='pdbligand=HZZ:[(2~{Z})-3,7-dimethylocta-2,6-dienyl]+dihydrogen+phosphate'>HZZ</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Flavin_prenyltransferase Flavin prenyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.129 2.5.1.129] </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=6qlv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qlv OCA], [https://pdbe.org/6qlv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6qlv RCSB], [https://www.ebi.ac.uk/pdbsum/6qlv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6qlv 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=6qlv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qlv OCA], [http://pdbe.org/6qlv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qlv RCSB], [http://www.ebi.ac.uk/pdbsum/6qlv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qlv ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/A0A072ZCW8_PSEAI A0A072ZCW8_PSEAI]] Flavin prenyltransferase that catalyzes the synthesis of the prenylated FMN cofactor (prenyl-FMN) for 4-hydroxy-3-polyprenylbenzoic acid decarboxylase UbiD. The prenyltransferase is metal-independent and links a dimethylallyl moiety from dimethylallyl monophosphate (DMAP) to the flavin N5 and C6 atoms of FMN.[HAMAP-Rule:MF_01984] | + | [https://www.uniprot.org/uniprot/A0A072ZCW8_PSEAI A0A072ZCW8_PSEAI] Flavin prenyltransferase that catalyzes the synthesis of the prenylated FMN cofactor (prenyl-FMN) for 4-hydroxy-3-polyprenylbenzoic acid decarboxylase UbiD. The prenyltransferase is metal-independent and links a dimethylallyl moiety from dimethylallyl monophosphate (DMAP) to the flavin N5 and C6 atoms of FMN.[HAMAP-Rule:MF_01984] |
| | <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: Flavin prenyltransferase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Leys, D]] | + | [[Category: Pseudomonas aeruginosa]] |
| - | [[Category: Marshall, S A]] | + | [[Category: Leys D]] |
| - | [[Category: Transferase]] | + | [[Category: Marshall SA]] |
| - | [[Category: Ubix prenyltransferase flavin binding]]
| + | |
| Structural highlights
6qlv is a 12 chain structure with sequence from Pseudomonas aeruginosa. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.391Å |
| Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
A0A072ZCW8_PSEAI Flavin prenyltransferase that catalyzes the synthesis of the prenylated FMN cofactor (prenyl-FMN) for 4-hydroxy-3-polyprenylbenzoic acid decarboxylase UbiD. The prenyltransferase is metal-independent and links a dimethylallyl moiety from dimethylallyl monophosphate (DMAP) to the flavin N5 and C6 atoms of FMN.[HAMAP-Rule:MF_01984]
Publication Abstract from PubMed
The UbiX-UbiD enzymes are widespread in microbes, acting in concert to decarboxylate alpha-beta unsaturated carboxylic acids using a highly modified flavin cofactor, prenylated FMN (prFMN). UbiX serves as the flavin prenyltransferase, extending the isoalloxazine ring system with a fourth non-aromatic ring, derived from sequential linkage between a dimethylallyl moiety and the FMN N5 and C6. Using structure determination and solution studies of both dimethylallyl monophosphate (DMAP) and dimethyallyl pyrophosphate (DMAPP) dependent UbiX enzymes, we reveal the first step, N5-C1' bond formation, is contingent on the presence of a dimethylallyl substrate moiety. Hence, an SN1 mechanism similar to other prenyltransferases is proposed. Selected variants of the (pyro)phosphate binding site are unable to catalyse subsequent Friedel-Crafts alkylation of the flavin C6, but can be rescued by addition of (pyro)phosphate. Thus, retention of the (pyro)phosphate leaving group is required for C6-C3' bond formation, resembling pyrophosphate initiated class I terpene cyclase reaction chemistry.
The UbiX flavin prenyltransferase reaction mechanism resembles class I terpene cyclase chemistry.,Marshall SA, Payne KAP, Fisher K, White MD, Ni Cheallaigh A, Balaikaite A, Rigby SEJ, Leys D Nat Commun. 2019 May 29;10(1):2357. doi: 10.1038/s41467-019-10220-1. PMID:31142738[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Marshall SA, Payne KAP, Fisher K, White MD, Ni Cheallaigh A, Balaikaite A, Rigby SEJ, Leys D. The UbiX flavin prenyltransferase reaction mechanism resembles class I terpene cyclase chemistry. Nat Commun. 2019 May 29;10(1):2357. doi: 10.1038/s41467-019-10220-1. PMID:31142738 doi:http://dx.doi.org/10.1038/s41467-019-10220-1
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