4rep: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4rep]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Nonlabens_dokdonensis_DSW-6 Nonlabens dokdonensis DSW-6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4REP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4REP FirstGlance]. <br>
<table><tr><td colspan='2'>[[4rep]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Nonlabens_dokdonensis_DSW-6 Nonlabens dokdonensis DSW-6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4REP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4REP FirstGlance]. <br>
</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=GOL:GLYCEROL'>GOL</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]] 1.97&#8491;</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=GOL:GLYCEROL'>GOL</scene></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=4rep FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rep OCA], [https://pdbe.org/4rep PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rep RCSB], [https://www.ebi.ac.uk/pdbsum/4rep PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rep 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=4rep FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rep OCA], [https://pdbe.org/4rep PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rep RCSB], [https://www.ebi.ac.uk/pdbsum/4rep PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rep ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[https://www.uniprot.org/uniprot/CRTDH_NONDD CRTDH_NONDD] Catalyzes the introduction of a C-3,4 double bond into 1'-hydroxy-gamma-carotene and rhodopin (1-hydroxylycopene) to yield 1'-hydroxytorulene and (3E)-3,4-didehydrorhodopin, respectively (By similarity). Can also use 1-hydroxy-all-trans-1,2-dihydro-neurosporene, 1,1'-dihydroxy-1,1',2,2'-tetrahydroneurosporene and 1,1'-dihydroxy-1,1',2,2'-tetrahydrolycopene (By similarity). Probably involved in the synthesis of myxol, a gamma-carotene derivative (Probable). May use FAD as a proton acceptor (Probable).[UniProtKB:Q7WT72]<ref>PMID:26138397</ref>  
[https://www.uniprot.org/uniprot/CRTDH_NONDD CRTDH_NONDD] Catalyzes the introduction of a C-3,4 double bond into 1'-hydroxy-gamma-carotene and rhodopin (1-hydroxylycopene) to yield 1'-hydroxytorulene and (3E)-3,4-didehydrorhodopin, respectively (By similarity). Can also use 1-hydroxy-all-trans-1,2-dihydro-neurosporene, 1,1'-dihydroxy-1,1',2,2'-tetrahydroneurosporene and 1,1'-dihydroxy-1,1',2,2'-tetrahydrolycopene (By similarity). Probably involved in the synthesis of myxol, a gamma-carotene derivative (Probable). May use FAD as a proton acceptor (Probable).[UniProtKB:Q7WT72]<ref>PMID:26138397</ref>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The gamma-carotenoids, such as myxol and saproxanthin, have a high potential to be utilized in nutraceutical and pharmaceutical industries for their neuro-protective and antioxidant effects. CrtD is involved in the production of gamma-carotenoids by desaturating the C3'-C4' position of 1'-OH-gamma-carotenoid. We determined the crystal structure of CrtD from Nonlabens dokdonensis DSW-6 (NdCrtD), the first structure of CrtD family enzymes. The NdCrtD structure was composed of two distinct domains, an FAD-binding domain and a substrate-binding domain, and the substrate-binding domain can be divided into two subdomains, a Rossmann fold-like subdomain and a lid subdomain. Although the FAD-binding domain showed a structure similar to canonical FAD-containing enzymes, the substrate-binding domain exhibited a novel structure to constitute a long and hydrophobic tunnel with a length of approximately 40A. The molecular docking-simulation reveals that the tunnel provides an appropriate substrate-binding site for the carotenoid such as 1'-OH-gamma-carotene with a length of approximately 35A. We could predict residues related to recognize the 1'-hydroxyl group and to stabilize the hydrophobic end without hydroxyl group. Moreover, we suggest that the flexible entrance loop may undergo an open-closed formational change during the binding of the substrate.
Crystal structure of 1'-OH-carotenoid 3,4-desaturase from Nonlabens dokdonensis DSW-6.,Ahn JW, Kim KJ Enzyme Microb Technol. 2015 Sep;77:29-37. doi: 10.1016/j.enzmictec.2015.05.005., Epub 2015 May 22. PMID:26138397<ref>PMID:26138397</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4rep" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>

Latest revision as of 15:51, 1 March 2024

Crystal Structure of gamma-carotenoid desaturaseCrystal Structure of gamma-carotenoid desaturase

Structural highlights

4rep is a 1 chain structure with sequence from Nonlabens dokdonensis DSW-6. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.97Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CRTDH_NONDD Catalyzes the introduction of a C-3,4 double bond into 1'-hydroxy-gamma-carotene and rhodopin (1-hydroxylycopene) to yield 1'-hydroxytorulene and (3E)-3,4-didehydrorhodopin, respectively (By similarity). Can also use 1-hydroxy-all-trans-1,2-dihydro-neurosporene, 1,1'-dihydroxy-1,1',2,2'-tetrahydroneurosporene and 1,1'-dihydroxy-1,1',2,2'-tetrahydrolycopene (By similarity). Probably involved in the synthesis of myxol, a gamma-carotene derivative (Probable). May use FAD as a proton acceptor (Probable).[UniProtKB:Q7WT72][1]

References

  1. ↑ Ahn JW, Kim KJ. Crystal structure of 1'-OH-carotenoid 3,4-desaturase from Nonlabens dokdonensis DSW-6. Enzyme Microb Technol. 2015 Sep;77:29-37. doi: 10.1016/j.enzmictec.2015.05.005., Epub 2015 May 22. PMID:26138397 doi:http://dx.doi.org/10.1016/j.enzmictec.2015.05.005

4rep, resolution 1.97Å

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