4ubs

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:01, 20 March 2024) (edit) (undo)
 
(2 intermediate revisions not shown.)
Line 1: Line 1:
==The crystal structure of cytochrome P450 105D7 from Streptomyces avermitilis in complex with Diclofenac==
==The crystal structure of cytochrome P450 105D7 from Streptomyces avermitilis in complex with Diclofenac==
-
<StructureSection load='4ubs' size='340' side='right' caption='[[4ubs]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+
<StructureSection load='4ubs' size='340' side='right'caption='[[4ubs]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[4ubs]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UBS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UBS FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[4ubs]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_avermitilis_MA-4680_=_NBRC_14893 Streptomyces avermitilis MA-4680 = NBRC 14893]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UBS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UBS FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DIF:2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC+ACID'>DIF</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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]] 2.2&#8491;</td></tr>
-
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pentalenic_acid_synthase Pentalenic acid synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.15.11 1.14.15.11] </span></td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DIF:2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC+ACID'>DIF</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=4ubs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ubs OCA], [http://pdbe.org/4ubs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ubs RCSB], [http://www.ebi.ac.uk/pdbsum/4ubs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ubs 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=4ubs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ubs OCA], [https://pdbe.org/4ubs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ubs RCSB], [https://www.ebi.ac.uk/pdbsum/4ubs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ubs ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
-
[[http://www.uniprot.org/uniprot/CYP28_STRAW CYP28_STRAW]] Catalyzes the conversion of 1-deoxypentalenic acid to pentalenic acid in the biosynthesis of neopentalenolactone antibiotic.<ref>PMID:21081950</ref>
+
[https://www.uniprot.org/uniprot/CYP28_STRAW CYP28_STRAW] Catalyzes the conversion of 1-deoxypentalenic acid to pentalenic acid in the biosynthesis of neopentalenolactone antibiotic.<ref>PMID:21081950</ref>
-
<div style="background-color:#fffaf0;">
+
-
== Publication Abstract from PubMed ==
+
-
Diclofenac is a nonsteroidal anti-inflammatory drug. It undergoes hydroxylation by mammalian cytochrome P450 enzymes at 4'- and/or 5'-positions. A bacterial P450 enzyme, CYP105D7 from Streptomyces avermitilis, has been shown to catalyze hydroxylation of 1-deoxypentalenic acid and an isoflavone daidzein. Here, we demonstrated that CYP105D7 also catalyzes hydroxylation of diclofenac at the C4'-position. A spectroscopic analysis showed that CYP105D7 binds diclofenac in a slightly cooperative manner with an affinity of 65 muM and a Hill coefficient of 1.16. The crystal structure of CYP105D7 in complex with diclofenac was determined at 2.2 A resolution. The distal pocket of CYP105D7 contains two diclofenac molecules, illustrating drug recognition with a double-ligand-binding mode. The C3' and C4' atoms of the dichlorophenyl ring of one diclofenac molecule are positioned near the heme iron, suggesting that it is positioned appropriately for aromatic hydroxylation to yield the 4'-hydroxylated product. However, recognition of diclofenac by CYP105D7 was completely different from that of rabbit CYP2C5, which binds one diclofenac molecule with a cluster of water molecules. The distal pocket of CYP105D7 contains four arginine residues, forming a wall of the substrate-binding pocket, and the arginine residues are conserved in bacterial P450s in the CYP105 family.
+
-
 
+
-
Structural basis for the 4'-hydroxylation of diclofenac by a microbial cytochrome P450 monooxygenase.,Xu LH, Ikeda H, Liu L, Arakawa T, Wakagi T, Shoun H, Fushinobu S Appl Microbiol Biotechnol. 2014 Oct 24. PMID:25341403<ref>PMID:25341403</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 4ubs" style="background-color:#fffaf0;"></div>
+
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Pentalenic acid synthase]]
+
[[Category: Large Structures]]
-
[[Category: Arakawa, T]]
+
[[Category: Streptomyces avermitilis MA-4680 = NBRC 14893]]
-
[[Category: Fushinobu, S]]
+
[[Category: Arakawa T]]
-
[[Category: Ikeda, H]]
+
[[Category: Fushinobu S]]
-
[[Category: Shoun, H]]
+
[[Category: Ikeda H]]
-
[[Category: Wakagi, T]]
+
[[Category: Shoun H]]
-
[[Category: Xu, L H]]
+
[[Category: Wakagi T]]
-
[[Category: Cytochrome p450]]
+
[[Category: Xu LH]]
-
[[Category: Diclofenac]]
+
-
[[Category: Hydroxylation]]
+
-
[[Category: Oxidoreductase]]
+

Current revision

The crystal structure of cytochrome P450 105D7 from Streptomyces avermitilis in complex with Diclofenac

PDB ID 4ubs

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4ubs"
Personal tools