7y3v: Difference between revisions

Revision as of 06:24, 7 April 2023

Crystal structure of CdpNPT in complex with harmane

Structural highlights

7y3v is a 4 chain structure with sequence from Aspergillus fumigatus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	CN9, PO4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CDNTP_ASPFM Prenyltransferase that catalyzes reverse prenylation at position N-1 of tryptophan-containing cyclic dipeptides (PubMed:17525915, PubMed:35767141, PubMed:18383240, PubMed:19113967, PubMed:19421461, PubMed:33643664). Accepts only dimethylallyl diphosphate (DMAPP) as the prenyl donor but shows broad substrate specificities toward its aromatic substrates (PubMed:17525915, PubMed:18383240, PubMed:19113967, PubMed:19421461, PubMed:33643664, PubMed:35767141). Shows also tryptophan aminopeptidase activity with preference for linear peptides containing a tryptophanyl moiety at the N-terminus (PubMed:18635009).^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7]

Publication Abstract from PubMed

The prenylation of compounds has attracted much attention, since it often adds bioactivity to non-prenylated compounds. We employed an enzyme assay with CdpNPT, an indole prenyltransferase from Aspergillus fumigatus with two naturally occurring beta-carbolines, harmine (3) and harman (4) as prenyl acceptors, in the presence of dimethylallyl diphosphate (DMAPP) as the prenyl donor. The enzyme accepted these two prenyl acceptor substrates to produce 6-(3',3'-dimethylallyl)harmine (5) from 3 and 9-(3',3'-dimethylallyl)harman (6) and 6-(3',3'-dimethylallyl)harman (7) from 4. The X-ray crystal structure analysis of the CdpNPT (38-440) truncated mutant complexed with 4, and docking simulation studies of DMAPP to the crystal structure of the CdpNPT (38-440) mutant, suggested that CdpNPT could employ the two-step prenylation mechanism to produce 7, while the enzyme produced 6 with either one- or two-step prenylation mechanisms. Furthermore, the antibacterial assays revealed that the 3',3'-dimethylallylation of 3 and 4, as well as harmol (1), at C-6 enhanced the activities against Staphylococcus aureus and Bacillus subtilis.

Catalytic potential of a fungal indole prenyltransferase toward beta-carbolines, harmine and harman, and their prenylation effects on antibacterial activity.,Hamdy SA, Kodama T, Nakashima Y, Han X, Morita H J Biosci Bioeng. 2022 Oct;134(4):311-317. doi: 10.1016/j.jbiosc.2022.07.004. Epub , 2022 Aug 2. PMID:35931602^[8]

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

References

↑ Yin WB, Ruan HL, Westrich L, Grundmann A, Li SM. CdpNPT, an N-prenyltransferase from Aspergillus fumigatus: overproduction, purification and biochemical characterisation. Chembiochem. 2007 Jul 9;8(10):1154-61. PMID:17525915 doi:10.1002/cbic.200700079
↑ Ruan HL, Yin WB, Wu JZ, Li SM. Reinvestigation of a cyclic dipeptide N-prenyltransferase reveals rearrangement of N-1 prenylated indole derivatives. Chembiochem. 2008 May 5;9(7):1044-7. PMID:18383240 doi:10.1002/cbic.200700723
↑ Kremer A, Li SM. Tryptophan aminopeptidase activity of several indole prenyltransferases from Aspergillus fumigatus. Chem Biol. 2008 Jul 21;15(7):729-38. PMID:18635009 doi:10.1016/j.chembiol.2008.05.019
↑ Zou H, Zheng X, Li SM. Substrate promiscuity of the cyclic dipeptide prenyltransferases from Aspergillus fumigatus ( section sign). J Nat Prod. 2009 Jan;72(1):44-52. PMID:19113967 doi:10.1021/np800501m
↑ Yin WB, Cheng J, Li SM. Stereospecific synthesis of aszonalenins by using two recombinant prenyltransferases. Org Biomol Chem. 2009 May 21;7(10):2202-7. doi: 10.1039/b902413a. Epub 2009 Apr , 3. PMID:19421461 doi:https://dx.doi.org/10.1039/b902413a
↑ Gardner ED, Dimas DA, Finneran MC, Brown SM, Burgett AW, Singh S. Indole C6 Functionalization of Tryprostatin B Using Prenyltransferase CdpNPT. Catalysts. 2020 Nov;10(11):1247. PMID:33643664 doi:10.3390/catal10111247
↑ Hamdy SA, Kodama T, Nakashima Y, Han X, Matsui T, Morita H. Enzymatic formation of a prenyl β-carboline by a fungal indole prenyltransferase. J Nat Med. 2022 Sep;76(4):873-879. PMID:35767141 doi:10.1007/s11418-022-01635-0
↑ Hamdy SA, Kodama T, Nakashima Y, Han X, Morita H. Catalytic potential of a fungal indole prenyltransferase toward β-carbolines, harmine and harman, and their prenylation effects on antibacterial activity. J Biosci Bioeng. 2022 Oct;134(4):311-317. PMID:35931602 doi:10.1016/j.jbiosc.2022.07.004

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Yin WB, Ruan HL, Westrich L, Grundmann A, Li SM. CdpNPT, an N-prenyltransferase from Aspergillus fumigatus: overproduction, purification and biochemical characterisation. Chembiochem. 2007 Jul 9;8(10):1154-61. PMID:17525915 doi:10.1002/cbic.200700079

[2] Ruan HL, Yin WB, Wu JZ, Li SM. Reinvestigation of a cyclic dipeptide N-prenyltransferase reveals rearrangement of N-1 prenylated indole derivatives. Chembiochem. 2008 May 5;9(7):1044-7. PMID:18383240 doi:10.1002/cbic.200700723

[3] Kremer A, Li SM. Tryptophan aminopeptidase activity of several indole prenyltransferases from Aspergillus fumigatus. Chem Biol. 2008 Jul 21;15(7):729-38. PMID:18635009 doi:10.1016/j.chembiol.2008.05.019

[4] Zou H, Zheng X, Li SM. Substrate promiscuity of the cyclic dipeptide prenyltransferases from Aspergillus fumigatus ( section sign). J Nat Prod. 2009 Jan;72(1):44-52. PMID:19113967 doi:10.1021/np800501m

[5] Yin WB, Cheng J, Li SM. Stereospecific synthesis of aszonalenins by using two recombinant prenyltransferases. Org Biomol Chem. 2009 May 21;7(10):2202-7. doi: 10.1039/b902413a. Epub 2009 Apr , 3. PMID:19421461 doi:https://dx.doi.org/10.1039/b902413a

[6] Gardner ED, Dimas DA, Finneran MC, Brown SM, Burgett AW, Singh S. Indole C6 Functionalization of Tryprostatin B Using Prenyltransferase CdpNPT. Catalysts. 2020 Nov;10(11):1247. PMID:33643664 doi:10.3390/catal10111247

[7] Hamdy SA, Kodama T, Nakashima Y, Han X, Matsui T, Morita H. Enzymatic formation of a prenyl β-carboline by a fungal indole prenyltransferase. J Nat Med. 2022 Sep;76(4):873-879. PMID:35767141 doi:10.1007/s11418-022-01635-0

[8] Hamdy SA, Kodama T, Nakashima Y, Han X, Morita H. Catalytic potential of a fungal indole prenyltransferase toward β-carbolines, harmine and harman, and their prenylation effects on antibacterial activity. J Biosci Bioeng. 2022 Oct;134(4):311-317. PMID:35931602 doi:10.1016/j.jbiosc.2022.07.004

[1]

[2]

[3]

[4]

[5]

[6]

[7]

[8]

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 7y3v is ON HOLD  until Paper Publication
+==Crystal structure of CdpNPT in complex with harmane==
+<StructureSection load='7y3v' size='340' side='right'caption='[[7y3v]], [[Resolution|resolution]] 2.43&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[7y3v]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_fumigatus Aspergillus fumigatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7Y3V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Y3V FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CN9:1-methyl-9H-pyrido[3,4-b]indole'>CN9</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=7y3v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7y3v OCA], [https://pdbe.org/7y3v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7y3v RCSB], [https://www.ebi.ac.uk/pdbsum/7y3v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7y3v ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CDNTP_ASPFM CDNTP_ASPFM] Prenyltransferase that catalyzes reverse prenylation at position N-1 of tryptophan-containing cyclic dipeptides (PubMed:17525915, PubMed:35767141, PubMed:18383240, PubMed:19113967, PubMed:19421461, PubMed:33643664). Accepts only dimethylallyl diphosphate (DMAPP) as the prenyl donor but shows broad substrate specificities toward its aromatic substrates (PubMed:17525915, PubMed:18383240, PubMed:19113967, PubMed:19421461, PubMed:33643664, PubMed:35767141). Shows also tryptophan aminopeptidase activity with preference for linear peptides containing a tryptophanyl moiety at the N-terminus (PubMed:18635009).<ref>PMID:17525915</ref> <ref>PMID:18383240</ref> <ref>PMID:18635009</ref> <ref>PMID:19113967</ref> <ref>PMID:19421461</ref> <ref>PMID:33643664</ref> <ref>PMID:35767141</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The prenylation of compounds has attracted much attention, since it often adds bioactivity to non-prenylated compounds. We employed an enzyme assay with CdpNPT, an indole prenyltransferase from Aspergillus fumigatus with two naturally occurring beta-carbolines, harmine (3) and harman (4) as prenyl acceptors, in the presence of dimethylallyl diphosphate (DMAPP) as the prenyl donor. The enzyme accepted these two prenyl acceptor substrates to produce 6-(3',3'-dimethylallyl)harmine (5) from 3 and 9-(3',3'-dimethylallyl)harman (6) and 6-(3',3'-dimethylallyl)harman (7) from 4. The X-ray crystal structure analysis of the CdpNPT (38-440) truncated mutant complexed with 4, and docking simulation studies of DMAPP to the crystal structure of the CdpNPT (38-440) mutant, suggested that CdpNPT could employ the two-step prenylation mechanism to produce 7, while the enzyme produced 6 with either one- or two-step prenylation mechanisms. Furthermore, the antibacterial assays revealed that the 3',3'-dimethylallylation of 3 and 4, as well as harmol (1), at C-6 enhanced the activities against Staphylococcus aureus and Bacillus subtilis.
-Authors:
+Catalytic potential of a fungal indole prenyltransferase toward beta-carbolines, harmine and harman, and their prenylation effects on antibacterial activity.,Hamdy SA, Kodama T, Nakashima Y, Han X, Morita H J Biosci Bioeng. 2022 Oct;134(4):311-317. doi: 10.1016/j.jbiosc.2022.07.004. Epub , 2022 Aug 2. PMID:35931602<ref>PMID:35931602</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 7y3v" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Aspergillus fumigatus]]
+[[Category: Large Structures]]
+[[Category: Morita H]]
+[[Category: Nakashima Y]]

7y3v: Difference between revisions

Revision as of 06:24, 7 April 2023

Crystal structure of CdpNPT in complex with harmane

Structural highlights

Function

Publication Abstract from PubMed

References

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