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3vsi

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Current revision

Crystal structure of native 1,6-APD (2-Animophenol-1,6-dioxygenase) complex with 4-Nitrocatechol

Structural highlights

3vsi is a 4 chain structure with sequence from Comamonas testosteroni CNB-1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.5Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

AMNA_COMTE Component of the 2-aminophenol 1,6-dioxygenase (APD) complex that catalyzes the ring fission of 2-aminophenol to produce 2-aminomuconic semialdehyde. CnbCa may have a role in the stability of the complex. The complex is also active on other substrates such as 2-amino-5-chlorophenol (68% activity), protocatechuate (33% activity) and catechol (5% activity). Both 2-aminophenol and 2-amino-5-cholorophenol are likely native substrates for this dioxygenase which is involved in the reductive degradation pathway of both nitrobenzene (NB) and 4-chloronitrobenzene (4-CNB), allowing C.testosteroni strain CNB-1 to grow on these compounds as sole source of carbon, nitrogen, and energy.^[1] ^[2]

Publication Abstract from PubMed

Dioxygen activation by nonhaem Fe(II) enzymes containing the 2-His-1-carboxylate facial triad has been extensively studied in recent years. Here, crystal structures of 2-aminophenol 1,6-dioxygenase, an enzyme that represents a minor group of extradiol dioxygenases and that catalyses the ring opening of 2-aminophenol, in complex with the lactone intermediate (4Z,6Z)-3-iminooxepin-2(3H)-one and the product 2-aminomuconic 6-semialdehyde and in complex with the suicide inhibitor 4-nitrocatechol are reported. The Fe-ligand binding schemes observed in these structures revealed some common geometrical characteristics that are shared by the published structures of extradiol dioxygenases, suggesting that enzymes that catalyse the oxidation of noncatecholic compounds are very likely to utilize a similar strategy for dioxygen activation and the fission of aromatic rings as the canonical mechanism. The Fe-ligation arrangement, however, is strikingly enantiomeric to that of all other 2-His-1-carboxylate enzymes apart from protocatechuate 4,5-dioxygenase. This structural variance leads to the generation of an uncommon O(-)-Fe(2+)-O(-) species prior to O(2) binding, which probably forms the structural basis on which APD distinguishes its specific substrate and inhibitor, which share an analogous molecular structure.

Structures of aminophenol dioxygenase in complex with intermediate, product and inhibitor.,Li de F, Zhang JY, Hou YJ, Liu L, Hu Y, Liu SJ, Wang da C, Liu W Acta Crystallogr D Biol Crystallogr. 2013 Jan;69(Pt 1):32-43. doi:, 10.1107/S0907444912042072. Epub 2012 Dec 20. PMID:23275161^[3]

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

References

↑ Wu JF, Sun CW, Jiang CY, Liu ZP, Liu SJ. A novel 2-aminophenol 1,6-dioxygenase involved in the degradation of p-chloronitrobenzene by Comamonas strain CNB-1: purification, properties, genetic cloning and expression in Escherichia coli. Arch Microbiol. 2005 Jan;183(1):1-8. Epub 2004 Dec 3. PMID:15580337 doi:http://dx.doi.org/10.1007/s00203-004-0738-5
↑ Wu JF, Jiang CY, Wang BJ, Ma YF, Liu ZP, Liu SJ. Novel partial reductive pathway for 4-chloronitrobenzene and nitrobenzene degradation in Comamonas sp. strain CNB-1. Appl Environ Microbiol. 2006 Mar;72(3):1759-65. PMID:16517619 doi:http://dx.doi.org/72/3/1759
↑ Li de F, Zhang JY, Hou YJ, Liu L, Hu Y, Liu SJ, Wang da C, Liu W. Structures of aminophenol dioxygenase in complex with intermediate, product and inhibitor. Acta Crystallogr D Biol Crystallogr. 2013 Jan;69(Pt 1):32-43. doi:, 10.1107/S0907444912042072. Epub 2012 Dec 20. PMID:23275161 doi:http://dx.doi.org/10.1107/S0907444912042072

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3vsi"

@@ Line 1: / Line 1: @@
 ==Crystal structure of native 1,6-APD (2-Animophenol-1,6-dioxygenase) complex with 4-Nitrocatechol==
-<StructureSection load='3vsi' size='340' side='right' caption='[[3vsi]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+<StructureSection load='3vsi' size='340' side='right'caption='[[3vsi]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3vsi]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Comamonas_testosteroni Comamonas testosteroni]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VSI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VSI FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3vsi]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Comamonas_testosteroni_CNB-1 Comamonas testosteroni CNB-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VSI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VSI FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4NC:4-NITROCATECHOL'>4NC</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</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]] 2.5&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3vsg|3vsg]], [[3vsh|3vsh]], [[3vsj|3vsj]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4NC:4-NITROCATECHOL'>4NC</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Protocatechuate_4,5-dioxygenase Protocatechuate 4,5-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.8 1.13.11.8] </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=3vsi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vsi OCA], [https://pdbe.org/3vsi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vsi RCSB], [https://www.ebi.ac.uk/pdbsum/3vsi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vsi ProSAT]</span></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=3vsi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vsi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vsi RCSB], [http://www.ebi.ac.uk/pdbsum/3vsi PDBsum]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/AMNA_COMTE AMNA_COMTE] Component of the 2-aminophenol 1,6-dioxygenase (APD) complex that catalyzes the ring fission of 2-aminophenol to produce 2-aminomuconic semialdehyde. CnbCa may have a role in the stability of the complex. The complex is also active on other substrates such as 2-amino-5-chlorophenol (68% activity), protocatechuate (33% activity) and catechol (5% activity). Both 2-aminophenol and 2-amino-5-cholorophenol are likely native substrates for this dioxygenase which is involved in the reductive degradation pathway of both nitrobenzene (NB) and 4-chloronitrobenzene (4-CNB), allowing C.testosteroni strain CNB-1 to grow on these compounds as sole source of carbon, nitrogen, and energy.<ref>PMID:15580337</ref> <ref>PMID:16517619</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 16: / Line 18: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3vsi" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Comamonas testosteroni]]
+[[Category: Comamonas testosteroni CNB-1]]
-[[Category: Protocatechuate 4,5-dioxygenase]]
+[[Category: Large Structures]]
-[[Category: Hou, Y J]]
+[[Category: Hou YJ]]
-[[Category: Hu, Y]]
+[[Category: Hu Y]]
-[[Category: Li, D F]]
+[[Category: Li DF]]
-[[Category: Liu, W]]
+[[Category: Liu W]]
-[[Category: Wang, D C]]
+[[Category: Wang DC]]
-[[Category: 2-his-1-carboxylate facial triad motif]]
-[[Category: Cnbc]]
-[[Category: Extradiol dioxygenase]]
-[[Category: Oxidoreductase-oxidoreductase inhibitor complex]]

3vsi

From Proteopedia

Current revision

Crystal structure of native 1,6-APD (2-Animophenol-1,6-dioxygenase) complex with 4-Nitrocatechol

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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