1nf8: Difference between revisions

Latest revision as of 07:55, 14 February 2024

Crystal structure of PhzD protein active site mutant with substrate

Structural highlights

1nf8 is a 1 chain structure with sequence from Pseudomonas aeruginosa. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.6Å
Ligands:	BOG, ISC
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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).^[1] ^[2] ^[3]

Evolutionary Conservation

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

References

↑ Parsons JF, Calabrese K, Eisenstein E, Ladner JE. Structure and mechanism of Pseudomonas aeruginosa PhzD, an isochorismatase from the phenazine biosynthetic pathway. Biochemistry. 2003 May 20;42(19):5684-93. PMID:12741825 doi:10.1021/bi027385d
↑ Recinos DA, Sekedat MD, Hernandez A, Cohen TS, Sakhtah H, Prince AS, Price-Whelan A, Dietrich LE. Redundant phenazine operons in Pseudomonas aeruginosa exhibit environment-dependent expression and differential roles in pathogenicity. Proc Natl Acad Sci U S A. 2012 Nov 20;109(47):19420-5. PMID:23129634 doi:10.1073/pnas.1213901109
↑ Mavrodi DV, Bonsall RF, Delaney SM, Soule MJ, Phillips G, Thomashow LS. Functional analysis of genes for biosynthesis of pyocyanin and phenazine-1-carboxamide from Pseudomonas aeruginosa PAO1. J Bacteriol. 2001 Nov;183(21):6454-65. PMID:11591691 doi:10.1128/JB.183.21.6454-6465.2001

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Parsons JF, Calabrese K, Eisenstein E, Ladner JE. Structure and mechanism of Pseudomonas aeruginosa PhzD, an isochorismatase from the phenazine biosynthetic pathway. Biochemistry. 2003 May 20;42(19):5684-93. PMID:12741825 doi:10.1021/bi027385d

[2] Recinos DA, Sekedat MD, Hernandez A, Cohen TS, Sakhtah H, Prince AS, Price-Whelan A, Dietrich LE. Redundant phenazine operons in Pseudomonas aeruginosa exhibit environment-dependent expression and differential roles in pathogenicity. Proc Natl Acad Sci U S A. 2012 Nov 20;109(47):19420-5. PMID:23129634 doi:10.1073/pnas.1213901109

[3] Mavrodi DV, Bonsall RF, Delaney SM, Soule MJ, Phillips G, Thomashow LS. Functional analysis of genes for biosynthesis of pyocyanin and phenazine-1-carboxamide from Pseudomonas aeruginosa PAO1. J Bacteriol. 2001 Nov;183(21):6454-65. PMID:11591691 doi:10.1128/JB.183.21.6454-6465.2001

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
-[[Image:1nf8.png|left|200px]]
-<!--
+==Crystal structure of PhzD protein active site mutant with substrate==
-The line below this paragraph, containing "STRUCTURE_1nf8", creates the "Structure Box" on the page.
+<StructureSection load='1nf8' size='340' side='right'caption='[[1nf8]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1nf8]] 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=1NF8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NF8 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#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=ISC:(5S,6S)-5-[(1-CARBOXYETHENYL)OXY]-6-HYDROXYCYCLOHEXA-1,3-DIENE-1-CARBOXYLIC+ACID'>ISC</scene></td></tr>
-{{STRUCTURE_1nf8|  PDB=1nf8  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1nf8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nf8 OCA], [https://pdbe.org/1nf8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nf8 RCSB], [https://www.ebi.ac.uk/pdbsum/1nf8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nf8 ProSAT]</span></td></tr>
+</table>
-===Crystal structure of PhzD protein active site mutant with substrate===
+== 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]]
-The line below this paragraph, {{ABSTRACT_PUBMED_12741825}}, adds the Publication Abstract to the page
+Check<jmol>
-(as it appears on PubMed at http://www.pubmed.gov), where 12741825 is the PubMed ID number.
+  <jmolCheckbox>
--->
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nf/1nf8_consurf.spt"</scriptWhenChecked>
-{{ABSTRACT_PUBMED_12741825}}
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
-==About this Structure==
+  </jmolCheckbox>
-[[1nf8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NF8 OCA].
+</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=1nf8 ConSurf].
+<div style="clear:both"></div>
-==Reference==
+== References ==
-<ref group="xtra">PMID:012741825</ref><references group="xtra"/>
+<references/>
-[[Category: Isochorismatase]]
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Pseudomonas aeruginosa]]
-[[Category: Calabrese, K.]]
+[[Category: Calabrese K]]
-[[Category: Eisenstein, E.]]
+[[Category: Eisenstein E]]
-[[Category: Ladner, J E.]]
+[[Category: Ladner JE]]
-[[Category: Parsons, F.]]
+[[Category: Parsons F]]
-[[Category: Enzyme]]
-[[Category: Hydrolase]]
-[[Category: Isochorismatase]]
-[[Category: Phenazine pathway]]

1nf8: Difference between revisions

Latest revision as of 07:55, 14 February 2024

Crystal structure of PhzD protein active site mutant with substrate

Structural highlights

Function

Evolutionary Conservation

References

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