000594783 001__ 594783
000594783 005__ 20250724132218.0
000594783 0247_ $$2doi$$a10.3389/fchem.2023.1220543
000594783 0247_ $$2datacite_doi$$a10.3204/PUBDB-2023-05960
000594783 0247_ $$2altmetric$$aaltmetric:152230155
000594783 0247_ $$2pmid$$a37593106
000594783 0247_ $$2WOS$$aWOS:001049107300001
000594783 0247_ $$2openalex$$aopenalex:W4385445342
000594783 037__ $$aPUBDB-2023-05960
000594783 041__ $$aEnglish
000594783 082__ $$a540
000594783 1001_ $$0P:(DE-H253)PIP1100107$$aKalkan, Ozlem$$b0
000594783 245__ $$aHeterologous expression, purification and structural features of native Dictyostelium discoideum dye-decolorizing peroxidase bound to a natively incorporated heme
000594783 260__ $$aLausanne$$bFrontiers Media$$c2023
000594783 3367_ $$2DRIVER$$aarticle
000594783 3367_ $$2DataCite$$aOutput Types/Journal article
000594783 3367_ $$0PUB:(DE-HGF)16$$2PUB:(DE-HGF)$$aJournal Article$$bjournal$$mjournal$$s1696935823_278292
000594783 3367_ $$2BibTeX$$aARTICLE
000594783 3367_ $$2ORCID$$aJOURNAL_ARTICLE
000594783 3367_ $$00$$2EndNote$$aJournal Article
000594783 520__ $$aThe Dictyostelium discoideum dye-decolorizing peroxidase (DdDyP) is a newly discovered peroxidase, which belongs to a unique class of heme peroxidase family that lacks homology to the known members of plant peroxidase superfamily. DdDyP catalyzes the H$_2$O$_2$-dependent oxidation of a wide-spectrum of substrates ranging from polycyclic dyes to lignin biomass, holding promise for potential industrial and biotechnological applications. To study the molecular mechanism of DdDyP, highly pure and functional protein with a natively incorporated heme is required, however, obtaining a functional DyP-type peroxidase with a natively bound heme is challenging and often requires addition of expensive biosynthesis precursors. Alternatively, a heme in vitro reconstitution approach followed by a chromatographic purification step to remove the excess heme is often used. Here, we show that expressing the DdDyP peroxidase in ×2 YT enriched medium at low temperature (20°C), without adding heme supplement or biosynthetic precursors, allows for a correct native incorporation of heme into the apo-protein, giving rise to a stable protein with a strong Soret peak at 402 nm. Further, we crystallized and determined the native structure of DdDyP at a resolution of 1.95 Å, which verifies the correct heme binding and its geometry. The structural analysis also reveals a binding of two water molecules at the distal site of heme plane bridging the catalytic residues (Arg239 and Asp149) of the GXXDG motif to the heme-Fe(III) via hydrogen bonds. Our results provide new insights into the geometry of native DdDyP active site and its implication on DyP catalysis. 
000594783 536__ $$0G:(DE-HGF)POF4-6G3$$a6G3 - PETRA III (DESY) (POF4-6G3)$$cPOF4-6G3$$fPOF IV$$x0
000594783 693__ $$0EXP:(DE-H253)P-P11-20150101$$1EXP:(DE-H253)PETRAIII-20150101$$6EXP:(DE-H253)P-P11-20150101$$aPETRA III$$fPETRA Beamline P11$$x0
000594783 7001_ $$0P:(DE-H253)PIP1098409$$aKantamneni, Sravya$$b1
000594783 7001_ $$0P:(DE-H253)PIP1093080$$aBrings, Lea$$b2
000594783 7001_ $$0P:(DE-H253)PIP1015711$$aHan, Huijong$$b3
000594783 7001_ $$0P:(DE-H253)PIP1016993$$aBean, Richard$$b4
000594783 7001_ $$0P:(DE-H253)PIP1006340$$aMancuso, Adrian$$b5
000594783 7001_ $$0P:(DE-HGF)0$$aKoua, Faisal H. M.$$b6$$eCorresponding author
000594783 773__ $$0PERI:(DE-600)2711776-5$$a10.3389/fchem.2023.1220543$$p1220543$$tFrontiers in Chemistry$$v11$$x2296-2646$$y2023
000594783 8564_ $$uhttps://bib-pubdb1.desy.de/record/594783/files/fchem-11-1220543.pdf$$yOpenAccess
000594783 8564_ $$uhttps://bib-pubdb1.desy.de/record/594783/files/fchem-11-1220543.pdf?subformat=pdfa$$xpdfa$$yOpenAccess
000594783 909CO $$ooai:bib-pubdb1.desy.de:594783$$pdnbdelivery$$pdriver$$pVDB$$popen_access$$popenaire
000594783 9101_ $$0I:(DE-588)1043621512$$6P:(DE-H253)PIP1100107$$aEuropean XFEL$$b0$$kXFEL.EU
000594783 9101_ $$0I:(DE-588)1043621512$$6P:(DE-H253)PIP1098409$$aEuropean XFEL$$b1$$kXFEL.EU
000594783 9101_ $$0I:(DE-588)1043621512$$6P:(DE-H253)PIP1093080$$aEuropean XFEL$$b2$$kXFEL.EU
000594783 9101_ $$0I:(DE-588)1043621512$$6P:(DE-H253)PIP1015711$$aEuropean XFEL$$b3$$kXFEL.EU
000594783 9101_ $$0I:(DE-588)1043621512$$6P:(DE-H253)PIP1016993$$aEuropean XFEL$$b4$$kXFEL.EU
000594783 9101_ $$0I:(DE-588)1043621512$$6P:(DE-H253)PIP1006340$$aEuropean XFEL$$b5$$kXFEL.EU
000594783 9101_ $$0I:(DE-HGF)0$$6P:(DE-H253)PIP1006340$$aExternal Institute$$b5$$kExtern
000594783 9101_ $$0I:(DE-588)1043621512$$6P:(DE-HGF)0$$aEuropean XFEL$$b6$$kXFEL.EU
000594783 9131_ $$0G:(DE-HGF)POF4-6G3$$1G:(DE-HGF)POF4-6G0$$2G:(DE-HGF)POF4-600$$3G:(DE-HGF)POF4$$4G:(DE-HGF)POF$$aDE-HGF$$bForschungsbereich Materie$$lGroßgeräte: Materie$$vPETRA III (DESY)$$x0
000594783 9141_ $$y2023
000594783 915__ $$0StatID:(DE-HGF)0160$$2StatID$$aDBCoverage$$bEssential Science Indicators$$d2022-11-30
000594783 915__ $$0LIC:(DE-HGF)CCBY4$$2HGFVOC$$aCreative Commons Attribution CC BY 4.0
000594783 915__ $$0StatID:(DE-HGF)0501$$2StatID$$aDBCoverage$$bDOAJ Seal$$d2021-05-13T10:38:39Z
000594783 915__ $$0StatID:(DE-HGF)0500$$2StatID$$aDBCoverage$$bDOAJ$$d2021-05-13T10:38:39Z
000594783 915__ $$0StatID:(DE-HGF)0113$$2StatID$$aWoS$$bScience Citation Index Expanded$$d2022-11-30
000594783 915__ $$0StatID:(DE-HGF)0700$$2StatID$$aFees$$d2022-11-30
000594783 915__ $$0StatID:(DE-HGF)0510$$2StatID$$aOpenAccess
000594783 915__ $$0StatID:(DE-HGF)0561$$2StatID$$aArticle Processing Charges$$d2022-11-30
000594783 915__ $$0StatID:(DE-HGF)0100$$2StatID$$aJCR$$bFRONT CHEM : 2022$$d2023-08-19
000594783 915__ $$0StatID:(DE-HGF)0200$$2StatID$$aDBCoverage$$bSCOPUS$$d2023-08-19
000594783 915__ $$0StatID:(DE-HGF)0300$$2StatID$$aDBCoverage$$bMedline$$d2023-08-19
000594783 915__ $$0StatID:(DE-HGF)0320$$2StatID$$aDBCoverage$$bPubMed Central$$d2023-08-19
000594783 915__ $$0StatID:(DE-HGF)0030$$2StatID$$aPeer Review$$bDOAJ : Anonymous peer review$$d2021-05-13T10:38:39Z
000594783 915__ $$0StatID:(DE-HGF)0199$$2StatID$$aDBCoverage$$bClarivate Analytics Master Journal List$$d2023-08-19
000594783 915__ $$0StatID:(DE-HGF)0150$$2StatID$$aDBCoverage$$bWeb of Science Core Collection$$d2023-08-19
000594783 915__ $$0StatID:(DE-HGF)1150$$2StatID$$aDBCoverage$$bCurrent Contents - Physical, Chemical and Earth Sciences$$d2023-08-19
000594783 915__ $$0StatID:(DE-HGF)9905$$2StatID$$aIF >= 5$$bFRONT CHEM : 2022$$d2023-08-19
000594783 9201_ $$0I:(DE-H253)HAS-User-20120731$$kDOOR ; HAS-User$$lDOOR-User$$x0
000594783 9201_ $$0I:(DE-H253)XFEL_E1_SPB_SFX-20210408$$kXFEL_E1_SPB/SFX$$lSPB/SFX$$x1
000594783 9201_ $$0I:(DE-H253)XFEL_E2_SEC-20210408$$kXFEL_E2_SEC$$lSample Environment and Characterisation$$x2
000594783 980__ $$ajournal
000594783 980__ $$aVDB
000594783 980__ $$aUNRESTRICTED
000594783 980__ $$aI:(DE-H253)HAS-User-20120731
000594783 980__ $$aI:(DE-H253)XFEL_E1_SPB_SFX-20210408
000594783 980__ $$aI:(DE-H253)XFEL_E2_SEC-20210408
000594783 9801_ $$aFullTexts