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.

4eht

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 07:12, 28 September 2022

Activator of the 2-Hydroxyisocaproyl-CoA dehydratase from Clostridium difficile with bound ADP

Structural highlights

4eht is a 2 chain structure with sequence from Clostridioides difficile. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[HADI_CLODI] Involved in the reductive branch of L-leucine fermentation. Required for the activation of (R)-2-hydroxyisocaproyl-CoA dehydratase. The reduced activator transfers one electron to the dehydratase concomitant with hydrolysis of ATP. This protein is extremely sensitive towards oxygen.^[1] ^[2]

Publication Abstract from PubMed

Members of the 2-hydroxyacyl-CoA dehydratase enzyme family catalyze the beta,alpha-dehydration of various CoA-esters in the fermentation of amino acids by clostridia. Abstraction of the non-acidic beta-proton of the 2-hydroxyacyl-CoA compounds is achieved by the reductive generation of ketyl radicals on the substrate, which is initiated by the transfer of an electron at low redox potentials. The highly energetic electron needed on the dehydratase is donated by a [4Fe-4S] cluster containing ATPase, termed activator. We investigated the activator of the 2-hydroxyisocaproyl-CoA dehydratase from Clostridium difficile. The activator is a homodimeric protein structurally related to acetate and sugar kinases, Hsc70 and actin, which has a [4Fe-4S] cluster bound in the dimer interface. The crystal structures of the Mg-ADP, Mg-ADPNP and nucleotide-free states of the reduced activator have been solved at 1.6 - 3.0 A resolution, allowing us to define the position of Mg2+ and water molecules in the vicinity of the nucleotides and the [4Fe-4S] cluster. The structures reveal redox- and nucleotide dependent changes agreeing with the modulation of the reduction potential of the [4Fe-4S] cluster by conformational changes. We also investigated the propensity of the activator to form a complex with its cognate dehydratase in the presence of Mg-ADP and Mg-ADPNP and together with the structural data present a refined mechanistic scheme for the ATP-dependent electron transfer between activator and dehydratase.

On the ATP-dependent Activation of the Radical Enzyme (R)-2-Hydroxyisocaproyl-CoA Dehydratase.,Knauer SH, Buckel W, Dobbek H Biochemistry. 2012 Jul 24. PMID:22827463^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Kim J, Darley D, Buckel W. 2-Hydroxyisocaproyl-CoA dehydratase and its activator from Clostridium difficile. FEBS J. 2005 Jan;272(2):550-61. doi: 10.1111/j.1742-4658.2004.04498.x. PMID:15654892 doi:http://dx.doi.org/10.1111/j.1742-4658.2004.04498.x
↑ Knauer SH, Buckel W, Dobbek H. On the ATP-dependent Activation of the Radical Enzyme (R)-2-Hydroxyisocaproyl-CoA Dehydratase. Biochemistry. 2012 Jul 24. PMID:22827463 doi:10.1021/bi300571z
↑ Knauer SH, Buckel W, Dobbek H. On the ATP-dependent Activation of the Radical Enzyme (R)-2-Hydroxyisocaproyl-CoA Dehydratase. Biochemistry. 2012 Jul 24. PMID:22827463 doi:10.1021/bi300571z

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4eht"

Categories: Clostridioides difficile | Large Structures | Dobbek H | Knauer SH

@@ Line 1: / Line 1: @@
 ==Activator of the 2-Hydroxyisocaproyl-CoA dehydratase from Clostridium difficile with bound ADP==
-<StructureSection load='4eht' size='340' side='right' caption='[[4eht]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
+<StructureSection load='4eht' size='340' side='right'caption='[[4eht]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4eht]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_difficilis"_hall_and_o'toole_1935 "bacillus difficilis" hall and o'toole 1935]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EHT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4EHT FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4eht]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridioides_difficile Clostridioides difficile]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EHT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4EHT FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ehu|4ehu]], [[4eia|4eia]]</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=4eht FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4eht OCA], [https://pdbe.org/4eht PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4eht RCSB], [https://www.ebi.ac.uk/pdbsum/4eht PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4eht ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">hadI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1496 "Bacillus difficilis" Hall and O'Toole 1935])</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=4eht FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4eht OCA], [http://pdbe.org/4eht PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4eht RCSB], [http://www.ebi.ac.uk/pdbsum/4eht PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4eht ProSAT]</span></td></tr>
 </table>
+== Function ==
+[[https://www.uniprot.org/uniprot/HADI_CLODI HADI_CLODI]] Involved in the reductive branch of L-leucine fermentation. Required for the activation of (R)-2-hydroxyisocaproyl-CoA dehydratase. The reduced activator transfers one electron to the dehydratase concomitant with hydrolysis of ATP. This protein is extremely sensitive towards oxygen.<ref>PMID:15654892</ref> <ref>PMID:22827463</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus difficilis hall and o'toole 1935]]
+[[Category: Clostridioides difficile]]
-[[Category: Dobbek, H]]
+[[Category: Large Structures]]
-[[Category: Knauer, S H]]
+[[Category: Dobbek H]]
-[[Category: 2-hydroxyisocaproyl-coa dehydratase binding]]
+[[Category: Knauer SH]]
-[[Category: Actin fold]]
-[[Category: Atp/adp binding]]
-[[Category: Atpase]]
-[[Category: Electron transfer]]
-[[Category: Electron transport]]

4eht

From Proteopedia

Revision as of 07:12, 28 September 2022

Activator of the 2-Hydroxyisocaproyl-CoA dehydratase from Clostridium difficile with bound ADP

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox