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2v7b

From Proteopedia

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Current revision

Crystal structures of a benzoate CoA ligase from Burkholderia xenovorans LB400

Structural highlights

2v7b is a 2 chain structure with sequence from Paraburkholderia xenovorans LB400. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.84Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q13WK3_PARXL

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

Xenobiotic aromatic compounds represent one of the most significant classes of environmental pollutants. A novel benzoate oxidation (box) pathway has been identified recently in Burkholderia xenovorans LB400 (referred to simply as LB400) that is capable of assimilating benzoate and intimately tied to the degradation of polychlorinated biphenyls (PCBs). The box pathway in LB400 is present in two paralogous copies (boxM and boxC) and encodes eight enzymes with the first committed step catalyzed by benzoate CoA ligase (BCL). As a first step towards delineating the biochemical role of the box pathway in LB400, we have carried out functional studies of the paralogous BCL enzymes (BCLM and BCLC) with 20 different putative substrates. We have established a structural rationale for the observed substrate specificities on the basis of a 1.84 A crystal structure of BCLM in complex with benzoate. These data show that, while BCLM and BCLC display similar overall substrate specificities, BCLM is significantly more active towards benzoate and 2-aminobenzoate with tighter binding (Km) and a faster reaction rate (Vmax). Despite these clear functional differences, the residues that define the substrate-binding site in BCLM are completely conserved in BCLC, suggesting that second shell residues may play a significant role in substrate recognition and catalysis. Furthermore, comparison of the active site of BCLM with the recently solved structures of 4-chlorobenzoate CoA ligase and 2, 3-dihydroxybenzoate CoA ligase offers additional insight into the molecular features that mediate substrate binding in adenylate-forming enzymes. This study provides the first biochemical characterization of a Box enzyme from LB400 and the first structural characterization of a Box enzyme from any organism, and further substantiates the concept of distinct roles for the two paralogous box pathways in LB400.

Biochemical and structural characterization of the paralogous benzoate CoA ligases from Burkholderia xenovorans LB400: defining the entry point into the novel benzoate oxidation (box) pathway.,Bains J, Boulanger MJ J Mol Biol. 2007 Nov 2;373(4):965-77. Epub 2007 Aug 19. PMID:17884091^[1]

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

References

↑ Bains J, Boulanger MJ. Biochemical and structural characterization of the paralogous benzoate CoA ligases from Burkholderia xenovorans LB400: defining the entry point into the novel benzoate oxidation (box) pathway. J Mol Biol. 2007 Nov 2;373(4):965-77. Epub 2007 Aug 19. PMID:17884091 doi:10.1016/j.jmb.2007.08.008

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2v7b"

Categories: Large Structures | Paraburkholderia xenovorans LB400 | Bains J | J Boulanger M

@@ Line 1: / Line 1: @@
-==CRYSTAL STRUCTURES OF A BENZOATE COA LIGASE FROM BURKHOLDERIA XENOVORANS LB400==
-<StructureSection load='2v7b' size='340' side='right' caption='[[2v7b]], [[Resolution|resolution]] 1.84&Aring;' scene=''>
+==Crystal structures of a benzoate CoA ligase from Burkholderia xenovorans LB400==
+<StructureSection load='2v7b' size='340' side='right'caption='[[2v7b]], [[Resolution|resolution]] 1.84&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2v7b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Burxl Burxl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V7B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V7B FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2v7b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Paraburkholderia_xenovorans_LB400 Paraburkholderia xenovorans LB400]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V7B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V7B FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</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]] 1.84&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Benzoate--CoA_ligase Benzoate--CoA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.25 6.2.1.25] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene></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=2v7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v7b OCA], [http://pdbe.org/2v7b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2v7b RCSB], [http://www.ebi.ac.uk/pdbsum/2v7b PDBsum]</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=2v7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v7b OCA], [https://pdbe.org/2v7b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v7b RCSB], [https://www.ebi.ac.uk/pdbsum/2v7b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v7b ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q13WK3_PARXL Q13WK3_PARXL]
 == 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/v7/2v7b_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/v7/2v7b_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 30: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Benzoate--CoA ligase]]
+[[Category: Large Structures]]
-[[Category: Burxl]]
+[[Category: Paraburkholderia xenovorans LB400]]
-[[Category: Bains, J]]
+[[Category: Bains J]]
-[[Category: Boulanger, M J]]
+[[Category: J Boulanger M]]
-[[Category: Benzoate coa ligase]]
-[[Category: Benzoate oxidation]]
-[[Category: Ligase]]

2v7b

From Proteopedia

Current revision

Crystal structures of a benzoate CoA ligase from Burkholderia xenovorans LB400

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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