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- EMDB-26357: CryoEM structure of the Candida albicans Aro1 dimer -

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Basic information

Entry
Database: EMDB / ID: EMD-26357
TitleCryoEM structure of the Candida albicans Aro1 dimer
Map dataMap from homogeneous refinement of full-length particles sharpened with DeepEMHancer
Sample
  • Complex: Aro1 dimer 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+) / 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 kinase activity / shikimate dehydrogenase (NADP+) / 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 / phosphorylation / 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 / EPSP synthase signature 1. / 3-phosphoshikimate 1-carboxyvinyltransferase / Shikimate dehydrogenase substrate binding, N-terminal / 3-phosphoshikimate 1-carboxyvinyltransferase, conserved site / Shikimate dehydrogenase substrate binding domain / 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: 4.16 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_26357.png

Downloads & links

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Map

FileDownload / File: emd_26357.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap from homogeneous refinement of full-length particles sharpened with DeepEMHancer
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)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2495 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.0017553907 - 2.1723437
Average (Standard dev.)0.00044715212 (±0.015780102)
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 homogeneous refinement of full-length particles

Fileemd_26357_additional_1.map
AnnotationRaw map from homogeneous refinement of full-length particles
Projections & Slices
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Additional map: Sharpened map from homogeneous refinement of full-length particles

Fileemd_26357_additional_2.map
AnnotationSharpened map from homogeneous refinement of full-length particles
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Additional map: Sharpened map from local refinement of DHQS/EPSPS chain...

Fileemd_26357_additional_3.map
AnnotationSharpened map from local refinement of DHQS/EPSPS chain A after EPSPS focused classification
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Additional map: Sharpened map from local refinement of DHQS/EPSPS chain...

Fileemd_26357_additional_4.map
AnnotationSharpened map from local refinement of DHQS/EPSPS chain B after EPSPS focused classification
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Additional map: Raw map from local refinement of DHQS/EPSPS chain...

Fileemd_26357_additional_5.map
AnnotationRaw map from local refinement of DHQS/EPSPS chain B after EPSPS focused classification
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AxesZYX

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Additional map: Raw map from local refinement of DHQS/EPSPS chain...

Fileemd_26357_additional_6.map
AnnotationRaw map from local refinement of DHQS/EPSPS chain A after EPSPS focused classification
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half map A from homogeneous refinement of full-length particles

Fileemd_26357_half_map_1.map
AnnotationHalf map A from homogeneous refinement of full-length particles
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half map B from homogeneous refinement of full-length particles

Fileemd_26357_half_map_2.map
AnnotationHalf map B from homogeneous refinement of full-length particles
Projections & Slices
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Sample components

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Entire : Aro1 dimer from Candida albicans

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

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Supramolecule #1: Aro1 dimer from Candida albicans

SupramoleculeName: Aro1 dimer 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 chloridesodium chlorida
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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / 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
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 83.5 e/Å2
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
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.16 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 87484
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: RIGID BODY FIT
Output model

PDB-7u5s:
CryoEM structure of the Candida albicans Aro1 dimer

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