1nqw: Difference between revisions
No edit summary |
No edit summary |
||
| Line 3: | Line 3: | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1nqw]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NQW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NQW FirstGlance]. <br> | <table><tr><td colspan='2'>[[1nqw]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NQW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NQW FirstGlance]. <br> | ||
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5YL:5-(6-D-RIBITYLAMINO-2,4(1H,3H)PYRIMIDINEDIONE-5-YL)+PENTYL-1-PHOSPHONIC+ACID'>5YL</scene>< | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5YL:5-(6-D-RIBITYLAMINO-2,4(1H,3H)PYRIMIDINEDIONE-5-YL)+PENTYL-1-PHOSPHONIC+ACID'>5YL</scene></td></tr> | ||
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1nqv|1nqv]], [[1nqu|1nqu]], [[1nqx|1nqx]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1nqv|1nqv]], [[1nqu|1nqu]], [[1nqx|1nqx]]</td></tr> | ||
<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/6,7-dimethyl-8-ribityllumazine_synthase 6,7-dimethyl-8-ribityllumazine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.78 2.5.1.78] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/6,7-dimethyl-8-ribityllumazine_synthase 6,7-dimethyl-8-ribityllumazine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.78 2.5.1.78] </span></td></tr> | ||
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1nqw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nqw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nqw RCSB], [http://www.ebi.ac.uk/pdbsum/1nqw PDBsum]</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=1nqw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nqw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nqw RCSB], [http://www.ebi.ac.uk/pdbsum/1nqw PDBsum]</span></td></tr> | ||
<table> | </table> | ||
== Function == | |||
[[http://www.uniprot.org/uniprot/RISB_AQUAE RISB_AQUAE]] Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin.<ref>PMID:12603336</ref> <ref>PMID:11237620</ref> | |||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
| Line 32: | Line 34: | ||
[[Category: 6,7-dimethyl-8-ribityllumazine synthase]] | [[Category: 6,7-dimethyl-8-ribityllumazine synthase]] | ||
[[Category: Aquifex aeolicus]] | [[Category: Aquifex aeolicus]] | ||
[[Category: Bacher, A | [[Category: Bacher, A]] | ||
[[Category: Cushman, M | [[Category: Cushman, M]] | ||
[[Category: Fischer, M | [[Category: Fischer, M]] | ||
[[Category: Haase, I | [[Category: Haase, I]] | ||
[[Category: Ladenstein, R | [[Category: Ladenstein, R]] | ||
[[Category: Meining, W | [[Category: Meining, W]] | ||
[[Category: Zhang, X | [[Category: Zhang, X]] | ||
[[Category: Catalytic mechanism]] | [[Category: Catalytic mechanism]] | ||
[[Category: Inhibitor complex]] | [[Category: Inhibitor complex]] | ||
Revision as of 15:40, 25 December 2014
Crystal Structure of Lumazine Synthase from Aquifex aeolicus in Complex with Inhibitor: 5-(6-D-ribitylamino-2,4(1H,3H)pyrimidinedione-5-yl)-1-pentyl-phosphonic acidCrystal Structure of Lumazine Synthase from Aquifex aeolicus in Complex with Inhibitor: 5-(6-D-ribitylamino-2,4(1H,3H)pyrimidinedione-5-yl)-1-pentyl-phosphonic acid
Structural highlights
Function[RISB_AQUAE] Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin.[1] [2] 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 PubMed6,7-Dimethyl-8-ribityllumazine is the biosynthetic precursor of riboflavin, which, as a coenzyme, plays a vital role in the electron transfer process for energy production in all cellular organisms. The enzymes involved in lumazine biosynthesis have been studied in considerable detail. However, the conclusive mechanism of the reaction catalyzed by lumazine synthase has remained unclear. Here, we report four crystal structures of the enzyme from the hyperthermophilic bacterium Aquifex aeolicus in complex with different inhibitor compounds. The structures were refined at resolutions of 1.72 A, 1.85 A, 2.05 A and 2.2 A, respectively. The inhibitors have been designed in order to mimic the substrate, the putative reaction intermediates and the final product. Structural comparisons of the native enzyme and the inhibitor complexes as well as the kinetic data of single-site mutants of lumazine synthase from Bacillus subtilis showed that several highly conserved residues at the active site, namely Phe22, His88, Arg127, Lys135 and Glu138 are most likely involved in catalysis. A structural model of the catalytic process, which illustrates binding of substrates, enantiomer specificity, proton abstraction/donation, inorganic phosphate elimination, formation of the Schiff base and cyclization is proposed. A structure-based model of the reaction catalyzed by lumazine synthase from Aquifex aeolicus.,Zhang X, Meining W, Cushman M, Haase I, Fischer M, Bacher A, Ladenstein R J Mol Biol. 2003 Apr 18;328(1):167-82. PMID:12684006[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
|
| ||||||||||||||||||||