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- EMDB-26359: Structure of the SK/DHQase/DHSD dimer from Candida albicans Aro1 -
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Open data
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Basic information
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Title | Structure of the SK/DHQase/DHSD dimer from Candida albicans Aro1 | |||||||||
![]() | Sharpened map from local refinement of SK/DHQase/DHSD | |||||||||
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![]() | BIOSYNTHETIC PROTEIN | |||||||||
Function / homology | ![]() 3-dehydroquinate synthase / 3-dehydroquinate synthase activity / shikimate kinase / shikimate dehydrogenase (NADP+) / shikimate kinase activity / 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase activity / shikimate 3-dehydrogenase (NADP+) activity / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity ...3-dehydroquinate synthase / 3-dehydroquinate synthase activity / shikimate kinase / shikimate dehydrogenase (NADP+) / shikimate kinase activity / 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase activity / shikimate 3-dehydrogenase (NADP+) activity / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / ATP binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.16 Å | |||||||||
![]() | Quade B / Borek D / Otwinowski Z | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular analysis and essentiality of Aro1 shikimate biosynthesis multi-enzyme in . Authors: Peter J Stogios / Sean D Liston / Cameron Semper / Bradley Quade / Karolina Michalska / Elena Evdokimova / Shane Ram / Zbyszek Otwinowski / Dominika Borek / Leah E Cowen / Alexei Savchenko / ![]() ![]() Abstract: In the human fungal pathogen , encodes an essential multi-enzyme that catalyses consecutive steps in the shikimate pathway for biosynthesis of chorismate, a precursor to folate and the aromatic ...In the human fungal pathogen , encodes an essential multi-enzyme that catalyses consecutive steps in the shikimate pathway for biosynthesis of chorismate, a precursor to folate and the aromatic amino acids. We obtained the first molecular image of Aro1 that reveals the architecture of all five enzymatic domains and their arrangement in the context of the full-length protein. Aro1 forms a flexible dimer allowing relative autonomy of enzymatic function of the individual domains. Our activity and in cellulo data suggest that only four of Aro1's enzymatic domains are functional and essential for viability of , whereas the 3-dehydroquinate dehydratase (DHQase) domain is inactive because of active site substitutions. We further demonstrate that in , the type II DHQase Dqd1 can compensate for the inactive DHQase domain of Aro1, suggesting an unrecognized essential role for this enzyme in shikimate biosynthesis. In contrast, in and , which do not encode a Dqd1 homolog, Aro1 DHQase domains are enzymatically active, highlighting diversity across species. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 229.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.2 KB 20.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.2 KB | Display | ![]() |
Images | ![]() | 117.1 KB | ||
Filedesc metadata | ![]() | 6.7 KB | ||
Others | ![]() ![]() ![]() | 123.4 MB 226.7 MB 226.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7u5uMC ![]() 6c5cC ![]() 7tbuC ![]() 7tbvC ![]() 7u5sC ![]() 7u5tC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | Sharpened map from local refinement of SK/DHQase/DHSD | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.2495 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Raw map from local refinement of SK/DHQase/DHSD
File | emd_26359_additional_1.map | ||||||||||||
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Annotation | Raw map from local refinement of SK/DHQase/DHSD | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A from local refinement of SK/DHQase/DHSD
File | emd_26359_half_map_1.map | ||||||||||||
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Annotation | Half map A from local refinement of SK/DHQase/DHSD | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B from local refinement of SK/DHQase/DHSD
File | emd_26359_half_map_2.map | ||||||||||||
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Annotation | Half map B from local refinement of SK/DHQase/DHSD | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Aro1 from Candida albicans
Entire | Name: Aro1 from Candida albicans |
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Components |
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-Supramolecule #1: Aro1 from Candida albicans
Supramolecule | Name: Aro1 from Candida albicans / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 169.4 KDa |
-Macromolecule #1: Pentafunctional AROM polypeptide
Macromolecule | Name: Pentafunctional AROM polypeptide / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: 3-dehydroquinate synthase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 169.59625 KDa |
Sequence | String: MSIEKVPILG KETIHVGYGI ADHIVREVIA NLASSTYVIV TDTNMARTPQ YSKLTDDFKT NLSEKRPESR LLTYCVSPGE NNKNRATKA AVEDFLLQQG CTRDTVILAV GGGVIGDMIG FVAATFMRGV RVVQVPTTLL AMVDSSVGGK TAIDTPLGKN F IGAFHQPE ...String: MSIEKVPILG KETIHVGYGI ADHIVREVIA NLASSTYVIV TDTNMARTPQ YSKLTDDFKT NLSEKRPESR LLTYCVSPGE NNKNRATKA AVEDFLLQQG CTRDTVILAV GGGVIGDMIG FVAATFMRGV RVVQVPTTLL AMVDSSVGGK TAIDTPLGKN F IGAFHQPE YVFCDVSFLE TLPARQFING MAEVVKTAAI WNEEEFTRLE NFSKKFLSVV TSKKPDLQSI KAELVKTVLE SV RVKAGVV SSDEKEAGLR NLLNFGHTIG HAIEAVLTPE ALHGECVSIG MIKEAELSRY LGILPPVAVA RLSKCLVAYG LPV SIDDKE FLKKVGPKRH YVEIDILLKK MAIDKKNDGS KIRCVLLEKI GKCYQLKAHQ VSKQDLSFVL TDEVLVHPFT NPPK ENIIV PPGSKSISNR ALILAALGNG TVRVKNLLHS DDTKHMLDAV ASLKGAEIST EDNGETIVVK GNGGNLVTSG EELYL GNAG TASRFLTTVA SLVGKSQASD DVILTGNARM QERPIGPLVD ALGSNGSEIE YLNKQGSLPL KISAGNGLKG GRIELA ATI SSQYVSSILM CAPYAKEPVT LALVGGKPIS QLYIDMTCAM MKSFGIEVTK STTEEYTYHI PKGTYKNPSE YVIESDA SS ATYPLAFAAM TGTSCTIPNI GSSSLQGDAK FAVDVLKPMG CKVEQTTTST TVTGPPRGHL KPLPHVDMEP MTDAFLTA S VVAAVAKGGS STSITGIANQ RVKECNRIEA MVTELAKFGV PANELPDGIE IHGIDIEDLK TPEISKRGVS SYDDHRVAM SFSLLAGLCK EPVLILERST TGKTWPGWWD ILHSKFKIEL DGYEPPFNTD KHVDKSSDKS IIVIGMRGTG KSTLSEWLAS FLGFKMLDM DKYLEEKLGT GIKSLIKAKG WEYFRQEEAI VAKECFTKFS KGYVLSTGGG IVEGEDARQQ LKSYADNGGI V LHLHRDLD ETVTFLAADT TRPAYSSEVQ EVWLRREKWY HECSNYHFYS SHCSTEDEFN HLRRSFVNYI KLITGAERPV VP AGRSAAV VLTSPDLNEV VGDLESITIG ADAVELRVDL FKDTSAEFVA AQIAVIRKHA DLPIIYTVRT VSQGGKFPDE NVD ELKSLL LLGIRLGVAY VDLQLTAPNE LIEEISSKKG FTRVIGTYQD INGELKWNNV EWKNKYNQGV SMNADIVRLV GKAN SIQDN LDLENFKKQN TLKPLIAFNL GSQGKLSQVL NGTFTPISHK LLPNDEEFLT IGELNQTYFD IGGFTAKKFW VIGSP IEHS RSPNLHNAGY KALNLPYQFG RFEATDVDVV YDNLINKPDF GGLAITMPLK LDIMKFATKL SDAAETIGAV NTLIPI EGG YFGDNTDWVG ISNSFIRAGV PPKSSSNGLV VGAGGTSRAA IYALHQMGCA KIYLVNRTAA KLEELVKSFP KDYNLEI VE TEQQADKASK VSLAVSCIPA DKPLDGEVLK KIERILSNGS EQSAGFKPTL LEASYKPRVT PIMKLTEEQY KWKVIPGV E MLVNQGDRQF KLHTGFTAPY EIIHRAVVEE UniProtKB: Pentafunctional AROM polypeptide |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 2.2 mg/mL | |||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 80 sec. / Pretreatment - Atmosphere: AIR | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 83.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |