3v1n: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older editNewer edit →
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,612 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,612 edits
No edit summary
Line 1: Line 1:
[[Image:3v1n.png|left|200px]]
==Crystal Structure of the H265Q mutant of a C-C hydrolase, BphD from Burkholderia xenovorans LB400, after exposure to its substrate HOPDA==
<StructureSection load='3v1n' size='340' side='right' caption='[[3v1n]], [[Resolution|resolution]] 1.59&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3v1n]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_xenovorans Burkholderia xenovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V1N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3V1N FirstGlance]. <br>
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene>, <scene name='pdbligand=HPK:(3E)-2,6-DIOXO-6-PHENYLHEX-3-ENOATE'>HPK</scene>, <scene name='pdbligand=MLA:MALONIC+ACID'>MLA</scene><br>
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2og1|2og1]], [[2ri6|2ri6]], [[2pu7|2pu7]], [[2puh|2puh]], [[2puj|2puj]], [[2rhw|2rhw]], [[2rht|2rht]], [[3v1k|3v1k]], [[3v1l|3v1l]], [[3v1m|3v1m]]</td></tr>
<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">bphD, Bxeno_C1120, Bxe_C1186 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=36873 Burkholderia xenovorans])</td></tr>
<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2,6-dioxo-6-phenylhexa-3-enoate_hydrolase 2,6-dioxo-6-phenylhexa-3-enoate hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.7.1.8 3.7.1.8] </span></td></tr>
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3v1n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v1n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3v1n RCSB], [http://www.ebi.ac.uk/pdbsum/3v1n PDBsum]</span></td></tr>
<table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Meta-cleavage product (MCP) hydrolases are members of the alpha/beta-hydrolase superfamily that utilize a Ser-His-Asp triad to catalyze the hydrolysis of a C-C bond. BphD, the MCP hydrolase from the biphenyl degradation pathway, hydrolyzes 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) to 2-hydroxypenta-2,4-dienoic acid (HPD) and benzoate. A 1.6 A resolution crystal structure of BphD H265Q incubated with HOPDA revealed that the enzyme's catalytic serine was benzoylated. The acyl-enzyme is stabilized by hydrogen bonding from the amide backbone of 'oxyanion hole' residues, consistent with formation of a tetrahedral oxyanion during nucleophilic attack by Ser112. Chemical quench and mass spectrometry studies substantiated the formation and decay of a Ser112-benzoyl species in wild-type BphD on a time scale consistent with turnover and incorporation of a single equivalent of (18)O into the benzoate produced during hydrolysis in H(2)(18)O. Rapid-scanning kinetic studies indicated that the catalytic histidine contributes to the rate of acylation by only an order of magnitude, but affects the rate of deacylation by over 5 orders of magnitude. The orange-colored catalytic intermediate, ES(red), previously detected in the wild-type enzyme and proposed herein to be a carbanion, was not observed during hydrolysis by H265Q. In the newly proposed mechanism, the carbanion abstracts a proton from Ser112, thereby completing tautomerization and generating a serinate for nucleophilic attack on the C6-carbonyl. Finally, quantification of an observed pre-steady-state kinetic burst suggests that BphD is a half-site reactive enzyme. While the updated catalytic mechanism shares features with the serine proteases, MCP hydrolase-specific chemistry highlights the versatility of the Ser-His-Asp triad.


<!--
Identification of an Acyl-Enzyme Intermediate in a meta-Cleavage Product Hydrolase Reveals the Versatility of the Catalytic Triad.,Ruzzini AC, Ghosh S, Horsman GP, Foster LJ, Bolin JT, Eltis LD J Am Chem Soc. 2012 Mar 14;134(10):4615-24. Epub 2012 Mar 5. PMID:22339283<ref>PMID:22339283</ref>
The line below this paragraph, containing "STRUCTURE_3v1n", creates the "Structure Box" on the page.
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
or leave the SCENE parameter empty for the default display.
-->
{{STRUCTURE_3v1n|  PDB=3v1n  |  SCENE=  }}


===Crystal Structure of the H265Q mutant of a C-C hydrolase, BphD from Burkholderia xenovorans LB400, after exposure to its substrate HOPDA===
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
 
</div>
 
== References ==
<!--
<references/>
The line below this paragraph, {{ABSTRACT_PUBMED_22339283}}, adds the Publication Abstract to the page
__TOC__
(as it appears on PubMed at http://www.pubmed.gov), where 22339283 is the PubMed ID number.
</StructureSection>
-->
{{ABSTRACT_PUBMED_22339283}}
 
==About this Structure==
[[3v1n]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_xenovorans Burkholderia xenovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V1N OCA].
 
==Reference==
<ref group="xtra">PMID:022339283</ref><references group="xtra"/>
[[Category: 2,6-dioxo-6-phenylhexa-3-enoate hydrolase]]
[[Category: 2,6-dioxo-6-phenylhexa-3-enoate hydrolase]]
[[Category: Burkholderia xenovorans]]
[[Category: Burkholderia xenovorans]]
Retrieved from "https://proteopedia.org/3v1n"