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- EMDB-26358: Structure of DHQS/EPSPS dimer from Candida albicans Aro1 -

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Basic information

Entry
Database: EMDB / ID: EMD-26358
TitleStructure of DHQS/EPSPS dimer from Candida albicans Aro1
Map dataSharpened map from focused refinement of DHQS/EPSPS region
Sample
  • Complex: Aro1 from Candida albicans
    • Protein or peptide: Pentafunctional AROM polypeptide
KeywordsBIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


3-dehydroquinate synthase / 3-dehydroquinate synthase activity / shikimate kinase / shikimate kinase activity / shikimate dehydrogenase (NADP+) / shikimate 3-dehydrogenase (NADP+) activity / 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase activity / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity ...3-dehydroquinate synthase / 3-dehydroquinate synthase activity / shikimate kinase / shikimate kinase activity / shikimate dehydrogenase (NADP+) / shikimate 3-dehydrogenase (NADP+) activity / 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase 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
Pentafunctional AroM protein / Shikimate dehydrogenase, AroM-type / 3-dehydroquinate synthase AroB / Quinate/shikimate 5-dehydrogenase/glutamyl-tRNA reductase / Shikimate / quinate 5-dehydrogenase / 3-dehydroquinate synthase domain / 3-dehydroquinate synthase / SDH, C-terminal / Shikimate 5'-dehydrogenase C-terminal domain / Shikimate kinase/Threonine synthase-like 1 ...Pentafunctional AroM protein / Shikimate dehydrogenase, AroM-type / 3-dehydroquinate synthase AroB / Quinate/shikimate 5-dehydrogenase/glutamyl-tRNA reductase / Shikimate / quinate 5-dehydrogenase / 3-dehydroquinate synthase domain / 3-dehydroquinate synthase / SDH, C-terminal / Shikimate 5'-dehydrogenase C-terminal domain / Shikimate kinase/Threonine synthase-like 1 / Shikimate kinase/gluconokinase / Shikimate kinase / 3-dehydroquinate dehydratase type I / Type I 3-dehydroquinase / Shikimate dehydrogenase substrate binding, N-terminal / Shikimate dehydrogenase substrate binding domain / EPSP synthase signature 1. / 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase, conserved site / EPSP synthase signature 2. / Enolpyruvate transferase domain / Enolpyruvate transferase domain superfamily / EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Aminoacid dehydrogenase-like, N-terminal domain superfamily / Aldolase-type TIM barrel / NAD(P)-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Pentafunctional AROM polypeptide
Similarity search - Component
Biological speciesCandida albicans (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsQuade B / Borek D / Otwinowski Z
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: Life Sci Alliance / Year: 2022
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
DepositionMar 2, 2022-
Header (metadata) releaseMay 4, 2022-
Map releaseMay 4, 2022-
UpdateFeb 14, 2024-
Current statusFeb 14, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26358.png

Downloads & links

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Map

FileDownload / File: emd_26358.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map from focused refinement of DHQS/EPSPS region
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 400 pix.
= 499.8 Å		1.25 Å/pix.
x 400 pix.
= 499.8 Å		1.25 Å/pix.
x 400 pix.
= 499.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2495 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.211
Minimum - Maximum-0.89735025 - 1.6080891
Average (Standard dev.)-0.00005482501 (±0.023081033)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 499.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Raw map from focused refinement of DHQS/EPSPS region

Fileemd_26358_additional_1.map
AnnotationRaw map from focused refinement of DHQS/EPSPS region
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Postprocessed map of DHQS and EPSPS region from...

Fileemd_26358_additional_2.map
AnnotationPostprocessed map of DHQS and EPSPS region from broken particles at 2.94A. Used for model building.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B from focused refinement of DHQS/EPSPS region

Fileemd_26358_half_map_1.map
AnnotationHalf map B from focused refinement of DHQS/EPSPS region
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A from focused refinement of DHQS/EPSPS region

Fileemd_26358_half_map_2.map
AnnotationHalf map A from focused refinement of DHQS/EPSPS region
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Aro1 from Candida albicans

EntireName: Aro1 from Candida albicans
Components
  • Complex: Aro1 from Candida albicans
    • Protein or peptide: Pentafunctional AROM polypeptide

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Supramolecule #1: Aro1 from Candida albicans

SupramoleculeName: Aro1 from Candida albicans / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Candida albicans (yeast) / Strain: CaLC6830
Molecular weightTheoretical: 169.4 KDa

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Macromolecule #1: Pentafunctional AROM polypeptide

MacromoleculeName: Pentafunctional AROM polypeptide / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: 3-dehydroquinate synthase
Source (natural)Organism: Candida albicans (yeast) / Strain: SC5314 / ATCC MYA-2876
Molecular weightTheoretical: 169.59625 KDa
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.2 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
10.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
GridModel: 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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 83.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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 stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1312555
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 87484
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6c5c

source_name: PDB, initial_model_type: experimental model

7tbu

source_name: PDB, initial_model_type: experimental model

7tbv

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7u5t:
Structure of DHQS/EPSPS dimer from Candida albicans Aro1

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