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[[Image:1nf9.gif|left|200px]]<br /><applet load="1nf9" size="350" color="white" frame="true" align="right" spinBox="true"
caption="1nf9, resolution 1.50&Aring;" />
'''Crystal Structure of PhzD protein from Pseudomonas aeruginosa'''<br />


==Overview==
==Crystal Structure of PhzD protein from Pseudomonas aeruginosa==
PhzD from Pseudomonas aeruginosa is an isochorismatase involved in phenazine biosynthesis. Phenazines are antimicrobial compounds that provide Pseudomonas with a competitive advantage in certain environments and may be partly responsible for the persistence of Pseudomonas infections. In vivo, PhzD catalyzes the hydrolysis of the vinyl ether functional group of 2-amino-2-deoxyisochorismate, yielding pyruvate and trans-2,3-dihydro-3-hydroxyanthranilic acid, which is then utilized in the phenazine biosynthetic pathway. PhzD also catalyzes hydrolysis of the related vinyl ethers isochorismate, chorismate, and 4-amino-4-deoxychorismate. Here we report the 1.5 A crystal structure of native PhzD, and the 1.6 A structure of the inactive D38A variant in complex with isochorismate. The structures reveal that isochorismate binds to the PhzD active site in a trans-diaxial conformation, and superposition of the structures indicates that the methylene pyruvyl carbon of isochorismate is adjacent to the side chain carboxylate of aspartate 38. The proximity of aspartate 38 to isochorismate and the complete loss of activity resulting from the conversion of aspartate 38 to alanine suggest a mechanism in which the carboxylate acts as a general acid to protonate the substrate, yielding a carbocation/oxocarbonium ion that is then rapidly hydrated to form a hemiketal intermediate, which then decomposes spontaneously to products. The structure of PhzD is remarkably similar to other structures from a subfamily of alpha/beta-hydrolase enzymes that includes pyrazinamidase and N-carbamoylsarcosine amidohydrolase. However, PhzD catalyzes unrelated chemistry and lacks a nucleophilic cysteine found in its close structural relatives. The vinyl ether hydrolysis catalyzed by PhzD represents yet another example of the catalytic diversity seen in the alpha/beta-hydrolase family, whose members are also known to hydrolyze amides, phosphates, phosphonates, epoxides, and C-X bonds.
<StructureSection load='1nf9' size='340' side='right'caption='[[1nf9]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[1nf9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NF9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NF9 FirstGlance]. <br>
1NF9 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa] with <scene name='pdbligand=BOG:'>BOG</scene> and <scene name='pdbligand=FMT:'>FMT</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Isochorismatase Isochorismatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.3.2.1 3.3.2.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NF9 OCA].
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5&#8491;</td></tr>
 
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene></td></tr>
==Reference==
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1nf9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nf9 OCA], [https://pdbe.org/1nf9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nf9 RCSB], [https://www.ebi.ac.uk/pdbsum/1nf9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nf9 ProSAT]</span></td></tr>
Structure and mechanism of Pseudomonas aeruginosa PhzD, an isochorismatase from the phenazine biosynthetic pathway., Parsons JF, Calabrese K, Eisenstein E, Ladner JE, Biochemistry. 2003 May 20;42(19):5684-93. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12741825 12741825]
</table>
[[Category: Isochorismatase]]
== Function ==
[https://www.uniprot.org/uniprot/PHZD1_PSEAE PHZD1_PSEAE] Involved in the biosynthesis of the antibiotic phenazine, a nitrogen-containing heterocyclic molecule. PhzD1 (operon phzA1B1C1E1F1G1) has a role in the biosynthesis of the phenazine during planktonic growth (PubMed:23129634). Catalyzes the hydrolysis of the vinyl ether functional group of 2-amino-2-deoxyisochorismate (ADIC), yielding pyruvate and trans-2,3-dihydro-3-hydroxyanthranilic acid (DHHA) (PubMed:12741825, PubMed:23129634). Also able to act on isochorismate, chorismate and 4-amino-4-deoxychorismate (ADC) as substrates (PubMed:12741825).<ref>PMID:12741825</ref> <ref>PMID:23129634</ref> <ref>PMID:11591691</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/nf/1nf9_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=1nf9 ConSurf].
<div style="clear:both"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Pseudomonas aeruginosa]]
[[Category: Pseudomonas aeruginosa]]
[[Category: Single protein]]
[[Category: Calabrese K]]
[[Category: Calabrese, K.]]
[[Category: Eisenstein E]]
[[Category: Eisenstein, E.]]
[[Category: Ladner JE]]
[[Category: Ladner, J E.]]
[[Category: Parsons F]]
[[Category: Parsons, F.]]
[[Category: BOG]]
[[Category: FMT]]
[[Category: enzyme]]
[[Category: isochorismatase]]
[[Category: phenazine pathway]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:05:26 2008''

Latest revision as of 07:55, 14 February 2024

Crystal Structure of PhzD protein from Pseudomonas aeruginosa

1nf9, resolution 1.50Å

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