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==Crystal structure of a bifunctional aldolase-dehydrogenase : sequestering a reactive and volatile intermediate==
==Crystal structure of a bifunctional aldolase-dehydrogenase : sequestering a reactive and volatile intermediate==
<StructureSection load='1nvm' size='340' side='right' caption='[[1nvm]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
<StructureSection load='1nvm' size='340' side='right'caption='[[1nvm]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1nvm]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseuf Pseuf]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NVM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NVM FirstGlance]. <br>
<table><tr><td colspan='2'>[[1nvm]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_sp._CF600 Pseudomonas sp. CF600]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NVM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NVM FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=OXL:OXALATE+ION'>OXL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DMPG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=79676 PSEUF]), DMPF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=79676 PSEUF])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=OXL:OXALATE+ION'>OXL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Acetaldehyde_dehydrogenase_(acetylating) Acetaldehyde dehydrogenase (acetylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.10 1.2.1.10] </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=1nvm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nvm OCA], [https://pdbe.org/1nvm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nvm RCSB], [https://www.ebi.ac.uk/pdbsum/1nvm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nvm ProSAT]</span></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=1nvm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nvm OCA], [http://pdbe.org/1nvm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nvm RCSB], [http://www.ebi.ac.uk/pdbsum/1nvm PDBsum]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/HOA_PSEUF HOA_PSEUF]] Catalyzes the retro-aldol cleavage of 4-hydroxy-2-oxopentanoate to pyruvate and acetaldehyde. Is involved in the meta-cleavage pathway for the degradation of aromatic compounds such as phenols, cresols and catechols.[HAMAP-Rule:MF_01656]<ref>PMID:1732207</ref> [[http://www.uniprot.org/uniprot/ACDH_PSEUF ACDH_PSEUF]] Catalyzes the conversion of acetaldehyde to acetyl-CoA, using NAD(+) and coenzyme A. Can also act on propanal and butanal to form propanoyl-CoA and butanoyl-CoA, respectively. Is the final enzyme in the meta-cleavage pathway for the degradation of aromatic compounds such as phenols, cresols and catechols. NADP(+) can replace NAD(+) but the rate of reaction is much slower.<ref>PMID:1732207</ref> 
[https://www.uniprot.org/uniprot/HOA_PSEUF HOA_PSEUF] Catalyzes the retro-aldol cleavage of 4-hydroxy-2-oxopentanoate to pyruvate and acetaldehyde. Is involved in the meta-cleavage pathway for the degradation of aromatic compounds such as phenols, cresols and catechols.[HAMAP-Rule:MF_01656]<ref>PMID:1732207</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/nv/1nvm_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nv/1nvm_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>
   </jmolCheckbox>
   </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/chain_selection.php?pdb_ID=2ata 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=1nvm ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The crystal structure of the bifunctional enzyme 4-hydroxy-2-ketovalerate aldolase (DmpG)/acylating acetaldehyde dehydrogenase (DmpF), which is involved in the bacterial degradation of toxic aromatic compounds, has been determined by multiwavelength anomalous dispersion (MAD) techniques and refined to 1.7-A resolution. Structures of the two polypeptides represent a previously unrecognized subclass of metal-dependent aldolases, and of a CoA-dependent dehydrogenase. The structure reveals a mixed state of NAD+ binding to the DmpF protomer. Domain movements associated with cofactor binding in the DmpF protomer may be correlated with channeling and activity at the DmpG protomer. In the presence of NAD+ a 29-A-long sequestered tunnel links the two active sites. Two barriers are visible along the tunnel and suggest control points for the movement of the reactive and volatile acetaldehyde intermediate between the two active sites.
Crystal structure of a bifunctional aldolase-dehydrogenase: sequestering a reactive and volatile intermediate.,Manjasetty BA, Powlowski J, Vrielink A Proc Natl Acad Sci U S A. 2003 Jun 10;100(12):6992-7. Epub 2003 May 22. PMID:12764229<ref>PMID:12764229</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1nvm" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Aldehyde dehydrogenase|Aldehyde dehydrogenase]]
*[[Aldehyde dehydrogenase 3D structures|Aldehyde dehydrogenase 3D structures]]
*[[Aldolase|Aldolase]]
*[[Aldolase 3D structures|Aldolase 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Pseuf]]
[[Category: Large Structures]]
[[Category: Manjasetty, A B]]
[[Category: Pseudomonas sp. CF600]]
[[Category: Powlowski, J]]
[[Category: Manjasetty AB]]
[[Category: Vrielink, A]]
[[Category: Powlowski J]]
[[Category: Bifunctional enzyme]]
[[Category: Vrielink A]]
[[Category: Lyase-oxidoreductase complex]]
[[Category: Sequestered tunnel]]
[[Category: Substrate channeling]]

Latest revision as of 07:59, 14 February 2024

Crystal structure of a bifunctional aldolase-dehydrogenase : sequestering a reactive and volatile intermediate

1nvm, resolution 1.70Å

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