|
|
| Line 1: |
Line 1: |
| | | | |
| | ==Crystal structure of CreD complex with fumarate== | | ==Crystal structure of CreD complex with fumarate== |
| - | <StructureSection load='5xnz' size='340' side='right' caption='[[5xnz]], [[Resolution|resolution]] 2.30Å' scene=''> | + | <StructureSection load='5xnz' size='340' side='right'caption='[[5xnz]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5xnz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"actinomyces_cremeus"_kudrina_in_gauze_et_al._1957 "actinomyces cremeus" kudrina in gauze et al. 1957]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XNZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XNZ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5xnz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_cremeus Streptomyces cremeus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XNZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XNZ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FUM:FUMARIC+ACID'>FUM</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]] 2.3Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">creD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=66881 "Actinomyces cremeus" Kudrina in Gauze et al. 1957])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FUM:FUMARIC+ACID'>FUM</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=5xnz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xnz OCA], [http://pdbe.org/5xnz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xnz RCSB], [http://www.ebi.ac.uk/pdbsum/5xnz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xnz 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=5xnz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xnz OCA], [https://pdbe.org/5xnz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xnz RCSB], [https://www.ebi.ac.uk/pdbsum/5xnz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xnz ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/A0A0K2JL82_9ACTN A0A0K2JL82_9ACTN] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 21: |
Line 23: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Actinomyces cremeus kudrina in gauze et al. 1957]] | + | [[Category: Large Structures]] |
| - | [[Category: Higashiyama, Y]] | + | [[Category: Streptomyces cremeus]] |
| - | [[Category: Katsuyama, Y]] | + | [[Category: Higashiyama Y]] |
| - | [[Category: Ohnishi, Y]] | + | [[Category: Katsuyama Y]] |
| - | [[Category: Sato, Y]] | + | [[Category: Ohnishi Y]] |
| - | [[Category: Senda, M]] | + | [[Category: Sato Y]] |
| - | [[Category: Senda, T]] | + | [[Category: Senda M]] |
| - | [[Category: Sugai, Y]] | + | [[Category: Senda T]] |
| - | [[Category: Cremeomycin]]
| + | [[Category: Sugai Y]] |
| - | [[Category: Fumarase]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Nitrous acid]]
| + | |
| Structural highlights
Function
A0A0K2JL82_9ACTN
Publication Abstract from PubMed
Enzymes belonging to the aspartase/fumarase superfamily catalyze elimination of various functional groups from succinate derivatives and play an important role in primary metabolism and aromatic compound degradation. Recently, an aspartase/fumarase superfamily enzyme, CreD, was discovered in cremeomycin biosynthesis. This enzyme catalyzes the elimination of nitrous acid from nitrosuccinate synthesized from aspartate by CreE, a flavin-dependent monooxygenase. Nitrous acid generated by this pathway is an important precursor of the diazo group of cremeomycin. CreD is the first aspartase/fumarase superfamily enzyme that was reported to catalyze the elimination of nitrous acid, and therefore we aimed to analyze its reaction mechanism. The crystal structure of CreD was determined by the molecular replacement native-single anomalous diffraction (MR native-SAD) method at 2.18 A resolution. Subsequently, the CreD-fumarate complex structure was determined at 2.30 A resolution by the soaking method. Similar to other aspartase/fumarase superfamily enzymes, the crystal structure of CreD was composed of three domains and formed a tetramer. Two molecules of fumarate were observed in one subunit of the CreD-fumarate complex. One of them was located in the active site pocket formed by three different subunits. Intriguingly, no histidine residue, which usually functions as a catalytic acid in aspartase/fumarase superfamily enzymes, was found around the fumarate molecule in the active site. Based on the mutational analysis, we propose a catalytic mechanism of CreD, in which Arg325 acts as a catalytic acid. This article is protected by copyright. All rights reserved.
Crystal structure of the nitrosuccinate lyase CreD in complex with fumarate provides insights into the catalytic mechanism for nitrous acid elimination.,Katsuyama Y, Sato Y, Sugai Y, Higashiyama Y, Senda M, Senda T, Ohnishi Y FEBS J. 2018 Mar 5. doi: 10.1111/febs.14429. PMID:29505698[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Katsuyama Y, Sato Y, Sugai Y, Higashiyama Y, Senda M, Senda T, Ohnishi Y. Crystal structure of the nitrosuccinate lyase CreD in complex with fumarate provides insights into the catalytic mechanism for nitrous acid elimination. FEBS J. 2018 Mar 5. doi: 10.1111/febs.14429. PMID:29505698 doi:http://dx.doi.org/10.1111/febs.14429
|
