2jcd

From Proteopedia

(Difference between revisions)

Current revision

Structure of the N-oxygenase AurF from Streptomyces thioluteus

Structural highlights

2jcd is a 2 chain structure with sequence from Streptomyces thioluteus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.11Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

AURF_STRTU Involved in the biosynthesis of the polyketide antibiotic aureothin (PubMed:14700630, PubMed:15038705). Catalyzes the oxidation of p-aminobenzoate (pABA) to p-nitrobenzoate (pNBA), an unusual polyketide synthase starter unit (PubMed:15038705, PubMed:16927313, PubMed:20798054, PubMed:18458342). Reaction mechanism involves the generation of a peroxodiiron(III/III) intermediate, which effects the initial oxidation of p-aminobenzoate to p-hydroxylaminobenzoate (Ar-NHOH) (PubMed:19731912, PubMed:20798054). Ar-NHOH is then probably directly converted to the fully oxidized p-nitrobenzoate via a four-electron N-oxidation, bypassing the formation of a nitroso compound (PubMed:20798054).^[1] ^[2] ^[3] ^[4] ^[5] ^[6]

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

Nitro groups are found in a number of bioactive compounds. Most of them arise by a stepwise mono-oxygenation of amino groups. One of the involved enzymes is AurF participating in the biosynthesis of aureothin. Its structure was established at 2.1 A resolution showing a homodimer with a binuclear manganese cluster. The enzyme preparation, which yielded the analyzed crystals, showed activity using in vitro and in vivo assays. Chain fold and cluster are homologous with ribonucleotide reductase subunit R2 and related enzymes. The two manganese ions and an iron content of about 15% were established by anomalous X-ray diffraction. A comparison of the cluster with more common di-iron clusters suggested an additional histidine in the coordination sphere to cause the preference for manganese over iron. There is no oxo-bridge. The substrate p-amino-benzoate was modeled into the active center. The model is supported by mutant activity measurements. It shows the geometry of the reaction and explains the established substrate spectrum.

Structure and action of the N-oxygenase AurF from Streptomyces thioluteus.,Zocher G, Winkler R, Hertweck C, Schulz GE J Mol Biol. 2007 Oct 12;373(1):65-74. Epub 2007 Jun 9. PMID:17765264^[7]

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

References

↑ He J, Hertweck C. Iteration as programmed event during polyketide assembly; molecular analysis of the aureothin biosynthesis gene cluster. Chem Biol. 2003 Dec;10(12):1225-32. PMID:14700630 doi:10.1016/j.chembiol.2003.11.009
↑ He J, Hertweck C. Biosynthetic origin of the rare nitroaryl moiety of the polyketide antibiotic aureothin: involvement of an unprecedented N-oxygenase. J Am Chem Soc. 2004 Mar 31;126(12):3694-5. PMID:15038705 doi:10.1021/ja039328t
↑ Simurdiak M, Lee J, Zhao H. A new class of arylamine oxygenases: evidence that p-aminobenzoate N-oxygenase (AurF) is a di-iron enzyme and further mechanistic studies. Chembiochem. 2006 Aug;7(8):1169-72. PMID:16927313 doi:10.1002/cbic.200600136
↑ Choi YS, Zhang H, Brunzelle JS, Nair SK, Zhao H. In vitro reconstitution and crystal structure of p-aminobenzoate N-oxygenase (AurF) involved in aureothin biosynthesis. Proc Natl Acad Sci U S A. 2008 May 13;105(19):6858-63. Epub 2008 May 5. PMID:18458342
↑ Korboukh VK, Li N, Barr EW, Bollinger JM Jr, Krebs C. A long-lived, substrate-hydroxylating peroxodiiron(III/III) intermediate in the amine oxygenase, AurF, from Streptomyces thioluteus. J Am Chem Soc. 2009 Sep 30;131(38):13608-9. PMID:19731912 doi:10.1021/ja9064969
↑ Li N, Korboukh VK, Krebs C, Bollinger JM Jr. Four-electron oxidation of p-hydroxylaminobenzoate to p-nitrobenzoate by a peroxodiferric complex in AurF from Streptomyces thioluteus. Proc Natl Acad Sci U S A. 2010 Sep 7;107(36):15722-7. PMID:20798054 doi:10.1073/pnas.1002785107
↑ Zocher G, Winkler R, Hertweck C, Schulz GE. Structure and action of the N-oxygenase AurF from Streptomyces thioluteus. J Mol Biol. 2007 Oct 12;373(1):65-74. Epub 2007 Jun 9. PMID:17765264 doi:10.1016/j.jmb.2007.06.014

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/2jcd"

@@ Line 3: / Line 3: @@
 <StructureSection load='2jcd' size='340' side='right'caption='[[2jcd]], [[Resolution|resolution]] 2.11&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2jcd]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JCD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JCD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2jcd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_thioluteus Streptomyces thioluteus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JCD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JCD FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 2.11&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></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=2jcd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jcd OCA], [https://pdbe.org/2jcd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jcd RCSB], [https://www.ebi.ac.uk/pdbsum/2jcd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jcd ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/AURF_STRTU AURF_STRTU] Involved in the biosynthesis of the polyketide antibiotic aureothin (PubMed:14700630, PubMed:15038705). Catalyzes the oxidation of p-aminobenzoate (pABA) to p-nitrobenzoate (pNBA), an unusual polyketide synthase starter unit (PubMed:15038705, PubMed:16927313, PubMed:20798054, PubMed:18458342). Reaction mechanism involves the generation of a peroxodiiron(III/III) intermediate, which effects the initial oxidation of p-aminobenzoate to p-hydroxylaminobenzoate (Ar-NHOH) (PubMed:19731912, PubMed:20798054). Ar-NHOH is then probably directly converted to the fully oxidized p-nitrobenzoate via a four-electron N-oxidation, bypassing the formation of a nitroso compound (PubMed:20798054).<ref>PMID:14700630</ref> <ref>PMID:15038705</ref> <ref>PMID:16927313</ref> <ref>PMID:18458342</ref> <ref>PMID:19731912</ref> <ref>PMID:20798054</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 31: / Line 34: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Hertweck, C]]
+[[Category: Streptomyces thioluteus]]
-[[Category: Schulz, G E]]
+[[Category: Hertweck C]]
-[[Category: Winkler, R]]
+[[Category: Schulz GE]]
-[[Category: Zocher, G E]]
+[[Category: Winkler R]]
-[[Category: Di-manganese mono-oxygenase]]
+[[Category: Zocher GE]]
-[[Category: N-oxygenase]]
-[[Category: Oxidation of p-benzoic acid]]
-[[Category: Oxidoreductase]]

2jcd

From Proteopedia

Current revision

Structure of the N-oxygenase AurF from Streptomyces thioluteus

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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