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New page: left|200px<br /><applet load="1nvm" size="450" color="white" frame="true" align="right" spinBox="true" caption="1nvm, resolution 1.70Å" /> '''Crystal structure of...
 
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[[Image:1nvm.jpg|left|200px]]<br /><applet load="1nvm" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1nvm, resolution 1.70&Aring;" />
'''Crystal structure of a bifunctional aldolase-dehydrogenase : sequestering a reactive and volatile intermediate'''<br />


==Overview==
==Crystal structure of a bifunctional aldolase-dehydrogenase : sequestering a reactive and volatile intermediate==
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.
<StructureSection load='1nvm' size='340' side='right'caption='[[1nvm]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
<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='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='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='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>
</table>
== Function ==
[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 ==
[[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/nv/1nvm_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=1nvm ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1NVM is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Pseudomonas_sp. Pseudomonas sp.] with MN, OXL, SO4, NAD and MPD as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1NVM OCA].
*[[Aldehyde dehydrogenase 3D structures|Aldehyde dehydrogenase 3D structures]]
 
*[[Aldolase 3D structures|Aldolase 3D structures]]
==Reference==
== References ==
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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12764229 12764229]
<references/>
[[Category: Acetaldehyde dehydrogenase (acetylating)]]
__TOC__
[[Category: Protein complex]]
</StructureSection>
[[Category: Pseudomonas sp.]]
[[Category: Large Structures]]
[[Category: Manjasetty, A.B.]]
[[Category: Pseudomonas sp. CF600]]
[[Category: Powlowski, J.]]
[[Category: Manjasetty AB]]
[[Category: Vrielink, A.]]
[[Category: Powlowski J]]
[[Category: MN]]
[[Category: Vrielink A]]
[[Category: MPD]]
[[Category: NAD]]
[[Category: OXL]]
[[Category: SO4]]
[[Category: bifunctional enzyme]]
[[Category: sequestered tunnel]]
[[Category: substrate channeling]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 22:35:39 2007''

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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