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4rep

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Revision as of 06:53, 2 March 2023

Crystal 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.
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]

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^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ 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
↑ 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

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4rep"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of gamma-carotenoid desaturase==
-<StructureSection load='4rep' size='340' side='right' caption='[[4rep]], [[Resolution|resolution]] 1.97&Aring;' scene=''>
+<StructureSection load='4rep' size='340' side='right'caption='[[4rep]], [[Resolution|resolution]] 1.97&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4rep]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Donghaeana_dokdonensis Donghaeana dokdonensis]. 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 [http://oca.weizmann.ac.il/oca-docs/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"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
+</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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DDD_2394 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=592029 Donghaeana dokdonensis])</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4rep FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rep OCA], [http://pdbe.org/4rep PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rep RCSB], [http://www.ebi.ac.uk/pdbsum/4rep PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4rep ProSAT]</span></td></tr>
 </table>
+== 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>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Donghaeana dokdonensis]]
+[[Category: Large Structures]]
-[[Category: Ahn, J W]]
+[[Category: Nonlabens dokdonensis DSW-6]]
-[[Category: Kim, E J]]
+[[Category: Ahn J-W]]
-[[Category: Kim, K J]]
+[[Category: Kim E-J]]
-[[Category: Kim, S]]
+[[Category: Kim K-J]]
-[[Category: Desaturase]]
+[[Category: Kim S]]
-[[Category: Fad-binding]]
-[[Category: Flavoprotein]]
-[[Category: Gamma-carotenoid desaturase]]
-[[Category: Oxidoreductase]]
-[[Category: Rossmann fold]]

4rep

From Proteopedia

Revision as of 06:53, 2 March 2023

Crystal Structure of gamma-carotenoid desaturase

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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