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6y1w

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Xcc4156, a flavin-dependent halogenase from Xanthomonas campestris

Structural highlights

6y1w is a 2 chain structure with sequence from Xanthomonas campestris pv. campestris str. B100. 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:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

B0RXY9_XANCB

Publication Abstract from PubMed

Flavin-dependent halogenases regioselectively introduce halide substituents into electron-rich substrates under mild reaction conditions. For the enzyme Xcc4156 from Xanthomonas campestris, the structure of a complex with the cofactor flavin adenine dinucleotide (FAD) and a bromide ion would be of particular interest as this enzyme exclusively brominates model substrates in vitro. Apo Xcc4156 crystals diffracted to 1.6 A resolution. The structure revealed an open substrate-binding site lacking the loop regions that close off the active site and contribute to substrate binding in tryptophan halogenases. Therefore, Xcc4156 might accept larger substrates, possibly even peptides. Soaking of apo Xcc4156 crystals with FAD led to crumbling of the intergrown crystals. Around half of the crystals soaked with FAD did not diffract, while in the others there was no electron density for FAD. The FAD-binding loop, which changes its conformation between the apo and the FAD-bound form in related enzymes, is involved in a crystal contact in the apo Xcc4156 crystals. The conformational change that is predicted to occur upon FAD binding would disrupt this crystal contact, providing a likely explanation for the destruction of the apo crystals in the presence of FAD. Soaking with only bromide did not result in bromide bound to the catalytic halide-binding site. Simultaneous soaking with FAD and bromide damaged the crystals more severely than soaking with only FAD. Together, these latter two observations suggest that FAD and bromide bind to Xcc4156 with positive cooperativity. Thus, apo Xcc4156 crystals provide functional insight into FAD and bromide binding, even though neither the cofactor nor the halide is visible in the structure.

Structure of apo flavin-dependent halogenase Xcc4156 hints at a reason for cofactor-soaking difficulties.,Widmann C, Ismail M, Sewald N, Niemann HH Acta Crystallogr D Struct Biol. 2020 Jul 1;76(Pt 7):687-697. doi:, 10.1107/S2059798320007731. Epub 2020 Jun 30. PMID:32627741^[1]

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

References

↑ Widmann C, Ismail M, Sewald N, Niemann HH. Structure of apo flavin-dependent halogenase Xcc4156 hints at a reason for cofactor-soaking difficulties. Acta Crystallogr D Struct Biol. 2020 Jul 1;76(Pt 7):687-697. doi:, 10.1107/S2059798320007731. Epub 2020 Jun 30. PMID:32627741 doi:http://dx.doi.org/10.1107/S2059798320007731

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/6y1w"

@@ Line 3: / Line 3: @@
 <StructureSection load='6y1w' size='340' side='right'caption='[[6y1w]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6y1w]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Xancb Xancb]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y1W OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6Y1W FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6y1w]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Xanthomonas_campestris_pv._campestris_str._B100 Xanthomonas campestris pv. campestris str. B100]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y1W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Y1W FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BU9:MESO-2,3-BUTANEDIOL'>BU9</scene>, <scene name='pdbligand=BUD:(2S,3S)-BUTANE-2,3-DIOL'>BUD</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</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]] 1.6&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">XCCB100_4156 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=509169 XANCB])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BU9:MESO-2,3-BUTANEDIOL'>BU9</scene>, <scene name='pdbligand=BUD:(2S,3S)-BUTANE-2,3-DIOL'>BUD</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6y1w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y1w OCA], [http://pdbe.org/6y1w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6y1w RCSB], [http://www.ebi.ac.uk/pdbsum/6y1w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6y1w ProSAT]</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=6y1w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y1w OCA], [https://pdbe.org/6y1w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6y1w RCSB], [https://www.ebi.ac.uk/pdbsum/6y1w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6y1w ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/B0RXY9_XANCB B0RXY9_XANCB]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 24: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Xancb]]
+[[Category: Xanthomonas campestris pv. campestris str. B100]]
-[[Category: Ismail, M]]
+[[Category: Ismail M]]
-[[Category: Niemann, H H]]
+[[Category: Niemann HH]]
-[[Category: Sewald, N]]
+[[Category: Sewald N]]
-[[Category: Widmann, C]]
+[[Category: Widmann C]]
-[[Category: Flavin-dependent halogenase]]
-[[Category: Flavoprotein]]

6y1w

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Xcc4156, a flavin-dependent halogenase from Xanthomonas campestris

Structural highlights

Function

Publication Abstract from PubMed

References

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