3ej3: Difference between revisions

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[[Image:3ej3.png|left|200px]]
==Structural and mechanistic analysis of trans-3-chloroacrylic acid dehalogenase activity==
<StructureSection load='3ej3' size='340' side='right' caption='[[3ej3]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3ej3]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_pavonaceae Pseudomonas pavonaceae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EJ3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EJ3 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=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ej7|3ej7]], [[3ej9|3ej9]]</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">caaD1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=47881 Pseudomonas pavonaceae]), caaD2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=47881 Pseudomonas pavonaceae])</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=3ej3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ej3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ej3 RCSB], [http://www.ebi.ac.uk/pdbsum/3ej3 PDBsum]</span></td></tr>
</table>
== 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/ej/3ej3_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/chain_selection.php?pdb_ID=2ata ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Trans-3-chloroacrylic acid dehalogenase (CaaD) is a critical enzyme in the trans-1,3-dichloropropene (DCP) degradation pathway in Pseudomonas pavonaceae 170. This enzyme allows bacteria to use trans-DCP, a common component in commercially produced fumigants, as a carbon source. CaaD specifically catalyzes the fourth step of the pathway by cofactor-independent dehalogenation of a vinyl carbon-halogen bond. Previous studies have reported an X-ray structure of CaaD under acidic conditions with a covalent modification of the catalytic betaPro1 residue. Here, the 1.7 A resolution X-ray structure of CaaD under neutral (pH 6.5) conditions is reported without the presence of the covalent adduct. In this new structure, a substrate-like acetate molecule is bound within the active site in a position analogous to the putative substrate-binding site. Additionally, a catalytically important water molecule was identified, consistent with previously proposed reaction schemes. Finally, flexibility of the catalytically relevant side chain alphaGlu52 is observed in the structure, supporting its role in the catalytic mechanism.


{{STRUCTURE_3ej3|  PDB=3ej3  |  SCENE=  }}
Structural and mechanistic analysis of trans-3-chloroacrylic acid dehalogenase activity.,Pegan SD, Serrano H, Whitman CP, Mesecar AD Acta Crystallogr D Biol Crystallogr. 2008 Dec;64(Pt 12):1277-82. Epub 2008, Nov 18. PMID:19018104<ref>PMID:19018104</ref>


===Structural and mechanistic analysis of trans-3-chloroacrylic acid dehalogenase activity===
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>


{{ABSTRACT_PUBMED_19018104}}
==See Also==
 
*[[Dehalogenase|Dehalogenase]]
==About this Structure==
== References ==
[[3ej3]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_pavonaceae Pseudomonas pavonaceae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EJ3 OCA].
<references/>
__TOC__
</StructureSection>
[[Category: Pseudomonas pavonaceae]]
[[Category: Pseudomonas pavonaceae]]
[[Category: Mesecar, A D.]]
[[Category: Mesecar, A D]]
[[Category: Pegan, S.]]
[[Category: Pegan, S]]
[[Category: Serrano, H.]]
[[Category: Serrano, H]]
[[Category: Whitman, C P.]]
[[Category: Whitman, C P]]
[[Category: Caad]]
[[Category: Caad]]
[[Category: Dehalogenase]]
[[Category: Dehalogenase]]

Revision as of 16:12, 19 November 2014

Structural and mechanistic analysis of trans-3-chloroacrylic acid dehalogenase activityStructural and mechanistic analysis of trans-3-chloroacrylic acid dehalogenase activity

Structural highlights

3ej3 is a 12 chain structure with sequence from Pseudomonas pavonaceae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:,
Gene:caaD1 (Pseudomonas pavonaceae), caaD2 (Pseudomonas pavonaceae)
Resources:FirstGlance, OCA, RCSB, PDBsum

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Trans-3-chloroacrylic acid dehalogenase (CaaD) is a critical enzyme in the trans-1,3-dichloropropene (DCP) degradation pathway in Pseudomonas pavonaceae 170. This enzyme allows bacteria to use trans-DCP, a common component in commercially produced fumigants, as a carbon source. CaaD specifically catalyzes the fourth step of the pathway by cofactor-independent dehalogenation of a vinyl carbon-halogen bond. Previous studies have reported an X-ray structure of CaaD under acidic conditions with a covalent modification of the catalytic betaPro1 residue. Here, the 1.7 A resolution X-ray structure of CaaD under neutral (pH 6.5) conditions is reported without the presence of the covalent adduct. In this new structure, a substrate-like acetate molecule is bound within the active site in a position analogous to the putative substrate-binding site. Additionally, a catalytically important water molecule was identified, consistent with previously proposed reaction schemes. Finally, flexibility of the catalytically relevant side chain alphaGlu52 is observed in the structure, supporting its role in the catalytic mechanism.

Structural and mechanistic analysis of trans-3-chloroacrylic acid dehalogenase activity.,Pegan SD, Serrano H, Whitman CP, Mesecar AD Acta Crystallogr D Biol Crystallogr. 2008 Dec;64(Pt 12):1277-82. Epub 2008, Nov 18. PMID:19018104[1]

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

See Also

References

  1. ↑ Pegan SD, Serrano H, Whitman CP, Mesecar AD. Structural and mechanistic analysis of trans-3-chloroacrylic acid dehalogenase activity. Acta Crystallogr D Biol Crystallogr. 2008 Dec;64(Pt 12):1277-82. Epub 2008, Nov 18. PMID:19018104 doi:http://dx.doi.org/S0907444908034707

3ej3, resolution 1.70Å

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