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.


1wmb

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="1wmb" size="450" color="white" frame="true" align="right" spinBox="true" caption="1wmb, resolution 2.0&Aring;" /> '''Crystal structure of ...)
Current revision (13:32, 13 March 2024) (edit) (undo)
 
(15 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1wmb.gif|left|200px]]<br /><applet load="1wmb" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1wmb, resolution 2.0&Aring;" />
 
-
'''Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase'''<br />
 
-
==Overview==
+
==Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase==
-
The gene coding for d-3-hydroxybutyrate dehydrogenase (HBDH) was cloned, from Pseudomonas fragi. The nucleotide sequence contained a 780 bp open, reading frame encoding a 260 amino acid residue protein. The recombinant, enzyme was efficiently expressed in Escherichia coli cells harboring, pHBDH11 and was purified to homogeneity as judged by SDS-PAGE. The enzyme, showed a strict stereospecificity to the D-enantiomer (3R-configuration), of 3-hydroxybutyrate as a substrate. Crystals of the ligand-free HBDH and, of the enzyme-NAD+ complex were obtained using the hanging-drop, vapor-diffusion method. The crystal structure of the HBDH was solved by, the multiwavelength anomalous diffraction method using the, SeMet-substituted enzyme and was refined to 2.0 A resolution. The overall, structure of P.fragi HBDH, including the catalytic tetrad of Asn114, Ser142, Tyr155, and Lys159, shows obvious relationships with other members, of the short-chain dehydrogenase/reductase (SDR) family. A cacodylate, anion was observed in both the ligand-free enzyme and the enzyme-NAD+, complex, and was located near the catalytic tetrad. It was shown that the, cacodylate inhibited the NAD+-dependent D-3-hydroxybutyrate, dehydrogenation competitively, with a Ki value of 5.6 mM. From the, interactions between cacodylate and the enzyme, it is predicted that, substrate specificity is achieved through the recognition of the 3-methyl, and carboxyl groups of the substrate.
+
<StructureSection load='1wmb' size='340' side='right'caption='[[1wmb]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
-
 
+
== Structural highlights ==
-
==About this Structure==
+
<table><tr><td colspan='2'>[[1wmb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_fragi Pseudomonas fragi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WMB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WMB FirstGlance]. <br>
-
1WMB is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_fragi Pseudomonas fragi] with MG and CAC as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/3-hydroxybutyrate_dehydrogenase 3-hydroxybutyrate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.30 1.1.1.30] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1WMB OCA].
+
</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&#8491;</td></tr>
-
 
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-
==Reference==
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1wmb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wmb OCA], [https://pdbe.org/1wmb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wmb RCSB], [https://www.ebi.ac.uk/pdbsum/1wmb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wmb ProSAT]</span></td></tr>
-
D-3-hydroxybutyrate dehydrogenase from Pseudomonas fragi: molecular cloning of the enzyme gene and crystal structure of the enzyme., Ito K, Nakajima Y, Ichihara E, Ogawa K, Katayama N, Nakashima K, Yoshimoto T, J Mol Biol. 2006 Jan 27;355(4):722-33. Epub 2005 Nov 14. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16325199 16325199]
+
</table>
-
[[Category: 3-hydroxybutyrate dehydrogenase]]
+
== Function ==
 +
[https://www.uniprot.org/uniprot/Q5KST5_PSEFR Q5KST5_PSEFR]
 +
== 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/wm/1wmb_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=1wmb ConSurf].
 +
<div style="clear:both"></div>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Large Structures]]
[[Category: Pseudomonas fragi]]
[[Category: Pseudomonas fragi]]
-
[[Category: Single protein]]
+
[[Category: Ichihara E]]
-
[[Category: Ichihara, E.]]
+
[[Category: Ito K]]
-
[[Category: Ito, K.]]
+
[[Category: Nakajima Y]]
-
[[Category: Nakajima, Y.]]
+
[[Category: Ogawa K]]
-
[[Category: Ogawa, K.]]
+
[[Category: Yoshimoto T]]
-
[[Category: Yoshimoto, T.]]
+
-
[[Category: CAC]]
+
-
[[Category: MG]]
+
-
[[Category: nad]]
+
-
[[Category: nadh]]
+
-
[[Category: oxidoreductase]]
+
-
[[Category: short chain dehydrogenase]]
+
-
 
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 00:14:39 2007''
+

Current revision

Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase

PDB ID 1wmb

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/1wmb"
Personal tools