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.


1p0f

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:04, 14 February 2024) (edit) (undo)
 
(12 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1p0f.jpg|left|200px]]
 
-
{{Structure
+
==Crystal Structure of the Binary Complex: NADP(H)-Dependent Vertebrate Alcohol Dehydrogenase (ADH8) with the cofactor NADP==
-
|PDB= 1p0f |SIZE=350|CAPTION= <scene name='initialview01'>1p0f</scene>, resolution 1.8&Aring;
+
<StructureSection load='1p0f' size='340' side='right'caption='[[1p0f]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>
+
<table><tr><td colspan='2'>[[1p0f]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pelophylax_perezi Pelophylax perezi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P0F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1P0F FirstGlance]. <br>
-
|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Alcohol_dehydrogenase_(NADP(+)) Alcohol dehydrogenase (NADP(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.2 1.1.1.2] </span>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
-
|GENE= ADH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=8403 Rana perezi])
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-
|DOMAIN=
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1p0f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p0f OCA], [https://pdbe.org/1p0f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1p0f RCSB], [https://www.ebi.ac.uk/pdbsum/1p0f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1p0f ProSAT]</span></td></tr>
-
|RELATEDENTRY=[[1p0c|1P0C]]
+
</table>
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1p0f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p0f OCA], [http://www.ebi.ac.uk/pdbsum/1p0f PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1p0f RCSB]</span>
+
== Function ==
-
}}
+
[https://www.uniprot.org/uniprot/ADH8_PELPE ADH8_PELPE]
 +
== 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/p0/1p0f_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=1p0f ConSurf].
 +
<div style="clear:both"></div>
-
'''Crystal Structure of the Binary Complex: NADP(H)-Dependent Vertebrate Alcohol Dehydrogenase (ADH8) with the cofactor NADP'''
+
==See Also==
-
 
+
*[[Alcohol dehydrogenase 3D structures|Alcohol dehydrogenase 3D structures]]
-
 
+
__TOC__
-
==Overview==
+
</StructureSection>
-
The amphibian enzyme ADH8, previously named class IV-like, is the only known vertebrate alcohol dehydrogenase (ADH) with specificity towards NADP(H). The three-dimensional structures of ADH8 and of the binary complex ADH8-NADP(+) have been now determined and refined to resolutions of 2.2A and 1.8A, respectively. The coenzyme and substrate specificity of ADH8, that has 50-65% sequence identity with vertebrate NAD(H)-dependent ADHs, suggest a role in aldehyde reduction probably as a retinal reductase. The large volume of the substrate-binding pocket can explain both the high catalytic efficiency of ADH8 with retinoids and the high K(m) value for ethanol. Preference of NADP(H) appears to be achieved by the presence in ADH8 of the triad Gly223-Thr224-His225 and the recruitment of conserved Lys228, which define a binding pocket for the terminal phosphate group of the cofactor. NADP(H) binds to ADH8 in an extended conformation that superimposes well with the NAD(H) molecules found in NAD(H)-dependent ADH complexes. No additional reshaping of the dinucleotide-binding site is observed which explains why NAD(H) can also be used as a cofactor by ADH8. The structural features support the classification of ADH8 as an independent ADH class.
+
[[Category: Large Structures]]
-
 
+
[[Category: Pelophylax perezi]]
-
==About this Structure==
+
[[Category: Farres J]]
-
1P0F is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Rana_perezi Rana perezi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P0F OCA].
+
[[Category: Fita I]]
-
 
+
[[Category: Ochoa WF]]
-
==Reference==
+
[[Category: Pares X]]
-
Crystal structure of the vertebrate NADP(H)-dependent alcohol dehydrogenase (ADH8)., Rosell A, Valencia E, Pares X, Fita I, Farres J, Ochoa WF, J Mol Biol. 2003 Jun 27;330(1):75-85. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12818203 12818203]
+
[[Category: Rosell A]]
-
[[Category: Alcohol dehydrogenase (NADP(+))]]
+
[[Category: Valencia E]]
-
[[Category: Rana perezi]]
+
-
[[Category: Single protein]]
+
-
[[Category: Farres, J.]]
+
-
[[Category: Fita, I.]]
+
-
[[Category: Ochoa, W F.]]
+
-
[[Category: Pares, X.]]
+
-
[[Category: Rosell, A.]]
+
-
[[Category: Valencia, E.]]
+
-
[[Category: adh topology]]
+
-
[[Category: nadp(h)-dependent]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:52:57 2008''
+

Current revision

Crystal Structure of the Binary Complex: NADP(H)-Dependent Vertebrate Alcohol Dehydrogenase (ADH8) with the cofactor NADP

PDB ID 1p0f

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/1p0f"
Personal tools