This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.


Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


2zbz

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (13:30, 1 November 2023) (edit) (undo)
 
(5 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2zbz.png|left|200px]]
 
-
{{STRUCTURE_2zbz| PDB=2zbz | SCENE= }}
+
==Crystal structure of vitamin D hydroxylase cytochrome P450 105A1 (R84A mutant) in complex with 1,25-dihydroxyvitamin D3==
 +
<StructureSection load='2zbz' size='340' side='right'caption='[[2zbz]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[2zbz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_griseolus Streptomyces griseolus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZBZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZBZ FirstGlance]. <br>
 +
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=VDX:5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANE-1,3-DIOL'>VDX</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=2zbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zbz OCA], [https://pdbe.org/2zbz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zbz RCSB], [https://www.ebi.ac.uk/pdbsum/2zbz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zbz ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/CPXE_STRGO CPXE_STRGO]
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zb/2zbz_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2zbz ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Vitamin D 3 (VD 3), a prohormone in mammals, plays a crucial role in the maintenance of calcium and phosphorus concentrations in serum. Activation of VD 3 requires 25-hydroxylation in the liver and 1alpha-hydroxylation in the kidney by cytochrome P450 (CYP) enzymes. Bacterial CYP105A1 converts VD 3 into 1alpha,25-dihydroxyvitamin D 3 (1alpha,25(OH) 2D 3) in two independent reactions, despite its low sequence identity with mammalian enzymes (&lt;21% identity). The present study determined the crystal structures of a highly active mutant (R84A) of CYP105A1 from Streptomyces griseolus in complex and not in complex with 1alpha,25(OH) 2D 3. The compound 1alpha,25(OH) 2D 3 is positioned 11 A from the iron atom along the I helix within the pocket. A similar binding mode is observed in the structure of the human CYP2R1-VD 3 complex, indicating a common substrate-binding mechanism for 25-hydroxylation. A comparison with the structure of wild-type CYP105A1 suggests that the loss of two hydrogen bonds in the R84A mutant increases the adaptability of the B' and F helices, creating a transient binding site. Further mutational analysis of the active site reveals that 25- and 1alpha-hydroxylations share residues that participate in these reactions. These results provide the structural basis for understanding the mechanism of the two-step hydroxylation that activates VD 3.
-
===Crystal structure of vitamin D hydroxylase cytochrome P450 105A1 (R84A mutant) in complex with 1,25-dihydroxyvitamin D3===
+
Crystal Structure of CYP105A1 (P450SU-1) in Complex with 1alpha,25-Dihydroxyvitamin D3(,).,Sugimoto H, Shinkyo R, Hayashi K, Yoneda S, Yamada M, Kamakura M, Ikushiro S, Shiro Y, Sakaki T Biochemistry. 2008 Apr 1;47(13):4017-27. Epub 2008 Mar 4. PMID:18314962<ref>PMID:18314962</ref>
-
{{ABSTRACT_PUBMED_18314962}}
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
 
+
</div>
-
==About this Structure==
+
<div class="pdbe-citations 2zbz" style="background-color:#fffaf0;"></div>
-
[[2zbz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_griseolus Streptomyces griseolus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZBZ OCA].
+
==See Also==
==See Also==
-
*[[Cytochrome P450|Cytochrome P450]]
+
*[[Cytochrome P450 3D structures|Cytochrome P450 3D structures]]
-
 
+
== References ==
-
==Reference==
+
<references/>
-
<ref group="xtra">PMID:018314962</ref><references group="xtra"/>
+
__TOC__
 +
</StructureSection>
 +
[[Category: Large Structures]]
[[Category: Streptomyces griseolus]]
[[Category: Streptomyces griseolus]]
-
[[Category: Unspecific monooxygenase]]
+
[[Category: Hayashi K]]
-
[[Category: Hayashi, K.]]
+
[[Category: Ikushiro S]]
-
[[Category: Ikushiro, S.]]
+
[[Category: Kamakura M]]
-
[[Category: Kamakura, M.]]
+
[[Category: Sakaki T]]
-
[[Category: Sakaki, T.]]
+
[[Category: Shinkyo R]]
-
[[Category: Shinkyo, R.]]
+
[[Category: Shiro Y]]
-
[[Category: Shiro, Y.]]
+
[[Category: Sugimoto H]]
-
[[Category: Sugimoto, H.]]
+
[[Category: Yamada M]]
-
[[Category: Yamada, M.]]
+
[[Category: Yoneda S]]
-
[[Category: Yoneda, S.]]
+
-
[[Category: Beta prism]]
+
-
[[Category: Heme]]
+
-
[[Category: Iron]]
+
-
[[Category: Metal-binding]]
+
-
[[Category: Monooxygenase]]
+
-
[[Category: Oxidoreductase]]
+
-
[[Category: P450]]
+

Current revision

Crystal structure of vitamin D hydroxylase cytochrome P450 105A1 (R84A mutant) in complex with 1,25-dihydroxyvitamin D3

PDB ID 2zbz

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Personal tools