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
Current revision (13:32, 13 March 2024) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1wmb.gif|left|200px]]
 
-
<!--
+
==Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase==
-
The line below this paragraph, containing "STRUCTURE_1wmb", creates the "Structure Box" on the page.
+
<StructureSection load='1wmb' size='340' side='right'caption='[[1wmb]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<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>
-
or leave the SCENE parameter empty for the default display.
+
</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>
-
{{STRUCTURE_1wmb| PDB=1wmb | SCENE= }}
+
<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>
-
 
+
</table>
-
'''Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase'''
+
== Function ==
-
 
+
[https://www.uniprot.org/uniprot/Q5KST5_PSEFR Q5KST5_PSEFR]
-
 
+
== Evolutionary Conservation ==
-
==Overview==
+
[[Image:Consurf_key_small.gif|200px|right]]
-
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.
+
Check<jmol>
-
 
+
<jmolCheckbox>
-
==About this Structure==
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wm/1wmb_consurf.spt"</scriptWhenChecked>
-
1WMB is a [[Single protein]] structure of sequence from [http://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].
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
 
+
<text>to colour the structure by Evolutionary Conservation</text>
-
==Reference==
+
</jmolCheckbox>
-
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://www.ncbi.nlm.nih.gov/pubmed/16325199 16325199]
+
</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].
-
[[Category: 3-hydroxybutyrate dehydrogenase]]
+
<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: Nad]]
+
-
[[Category: Nadh]]
+
-
[[Category: Oxidoreductase]]
+
-
[[Category: Short chain dehydrogenase]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 13:52:18 2008''
+

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