3dl9: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older editNewer edit →
No edit summary
No edit summary
Line 1: Line 1:


==Crystal structure of CYP2R1 in complex with 1-alpha-hydroxy-vitamin D2==
==Crystal structure of CYP2R1 in complex with 1-alpha-hydroxy-vitamin D2==
<StructureSection load='3dl9' size='340' side='right' caption='[[3dl9]], [[Resolution|resolution]] 2.72&Aring;' scene=''>
<StructureSection load='3dl9' size='340' side='right'caption='[[3dl9]], [[Resolution|resolution]] 2.72&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3dl9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DL9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DL9 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3dl9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DL9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DL9 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCD:BETA-CYCLODEXTRIN'>BCD</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=V2H:(1S,3R,5Z,7E,22E)-9,10-SECOERGOSTA-5,7,10,22-TETRAENE-1,3-DIOL'>V2H</scene></td></tr>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=V2H:(1S,3R,5Z,7E,22E)-9,10-SECOERGOSTA-5,7,10,22-TETRAENE-1,3-DIOL'>V2H</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3czh|3czh]]</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3czh|3czh]]</div></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CYP2R1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CYP2R1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=3dl9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dl9 OCA], [http://pdbe.org/3dl9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dl9 RCSB], [http://www.ebi.ac.uk/pdbsum/3dl9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3dl9 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=3dl9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dl9 OCA], [https://pdbe.org/3dl9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dl9 RCSB], [https://www.ebi.ac.uk/pdbsum/3dl9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dl9 ProSAT]</span></td></tr>
</table>
</table>
== Disease ==
== Disease ==
[[http://www.uniprot.org/uniprot/CP2R1_HUMAN CP2R1_HUMAN]] Defects in CYP2R1 are the cause of rickets vitamin D-dependent type 1B (VDDR1B) [MIM:[http://omim.org/entry/600081 600081]]; also known as pseudovitamin D(3) deficiency rickets due to 25-hydroxylase deficiency. A disorder caused by a selective deficiency of the active form of vitamin D (1,25-dihydroxyvitamin D3) and resulting in defective bone mineralization and clinical features of rickets. The patients sera have low calcium concentrations, low phosphate concentrations, elevated alkaline phosphatase activityand low levels of 25-hydroxyvitamin D.<ref>PMID:15128933</ref>   
[[https://www.uniprot.org/uniprot/CP2R1_HUMAN CP2R1_HUMAN]] Defects in CYP2R1 are the cause of rickets vitamin D-dependent type 1B (VDDR1B) [MIM:[https://omim.org/entry/600081 600081]]; also known as pseudovitamin D(3) deficiency rickets due to 25-hydroxylase deficiency. A disorder caused by a selective deficiency of the active form of vitamin D (1,25-dihydroxyvitamin D3) and resulting in defective bone mineralization and clinical features of rickets. The patients sera have low calcium concentrations, low phosphate concentrations, elevated alkaline phosphatase activityand low levels of 25-hydroxyvitamin D.<ref>PMID:15128933</ref>   
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/CP2R1_HUMAN CP2R1_HUMAN]] Has a D-25-hydroxylase activity on both forms of vitamin D, vitamin D(2) and D(3).<ref>PMID:12867411</ref> <ref>PMID:15465040</ref> <ref>PMID:18511070</ref>   
[[https://www.uniprot.org/uniprot/CP2R1_HUMAN CP2R1_HUMAN]] Has a D-25-hydroxylase activity on both forms of vitamin D, vitamin D(2) and D(3).<ref>PMID:12867411</ref> <ref>PMID:15465040</ref> <ref>PMID:18511070</ref>   
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dl/3dl9_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dl/3dl9_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
Line 23: Line 23:
</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=3dl9 ConSurf].
</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=3dl9 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
==See Also==
*[[Cytochrome P450 3D structures|Cytochrome P450 3D structures]]
== References ==
== References ==
<references/>
<references/>
Line 28: Line 31:
</StructureSection>
</StructureSection>
[[Category: Human]]
[[Category: Human]]
[[Category: Large Structures]]
[[Category: Arrowsmith, C H]]
[[Category: Arrowsmith, C H]]
[[Category: Bochkarev, A]]
[[Category: Bochkarev, A]]

Revision as of 11:01, 9 February 2022

Crystal structure of CYP2R1 in complex with 1-alpha-hydroxy-vitamin D2Crystal structure of CYP2R1 in complex with 1-alpha-hydroxy-vitamin D2

Structural highlights

3dl9 is a 2 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:, ,
Gene:CYP2R1 (HUMAN)
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

[CP2R1_HUMAN] Defects in CYP2R1 are the cause of rickets vitamin D-dependent type 1B (VDDR1B) [MIM:600081]; also known as pseudovitamin D(3) deficiency rickets due to 25-hydroxylase deficiency. A disorder caused by a selective deficiency of the active form of vitamin D (1,25-dihydroxyvitamin D3) and resulting in defective bone mineralization and clinical features of rickets. The patients sera have low calcium concentrations, low phosphate concentrations, elevated alkaline phosphatase activityand low levels of 25-hydroxyvitamin D.[1]

Function

[CP2R1_HUMAN] Has a D-25-hydroxylase activity on both forms of vitamin D, vitamin D(2) and D(3).[2] [3] [4]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  1. ↑ Cheng JB, Levine MA, Bell NH, Mangelsdorf DJ, Russell DW. Genetic evidence that the human CYP2R1 enzyme is a key vitamin D 25-hydroxylase. Proc Natl Acad Sci U S A. 2004 May 18;101(20):7711-5. Epub 2004 May 5. PMID:15128933 doi:10.1073/pnas.0402490101
  2. ↑ Cheng JB, Motola DL, Mangelsdorf DJ, Russell DW. De-orphanization of cytochrome P450 2R1: a microsomal vitamin D 25-hydroxilase. J Biol Chem. 2003 Sep 26;278(39):38084-93. Epub 2003 Jul 16. PMID:12867411 doi:10.1074/jbc.M307028200
  3. ↑ Shinkyo R, Sakaki T, Kamakura M, Ohta M, Inouye K. Metabolism of vitamin D by human microsomal CYP2R1. Biochem Biophys Res Commun. 2004 Nov 5;324(1):451-7. PMID:15465040 doi:S0006-291X(04)02115-1
  4. ↑ Strushkevich N, Usanov SA, Plotnikov AN, Jones G, Park HW. Structural analysis of CYP2R1 in complex with vitamin D3. J Mol Biol. 2008 Jun 27;380(1):95-106. Epub 2008 Apr 8. PMID:18511070 doi:10.1016/j.jmb.2008.03.065

3dl9, resolution 2.72Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=3dl9&oldid=3515224"