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- EMDB-80056: APS kinase from Entamoeba histolytica -

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Basic information

Entry
Database: EMDB / ID: EMD-80056
TitleAPS kinase from Entamoeba histolytica
Map data
Sample
  • Complex: homodimer
    • Protein or peptide: APS kinase Entamoeba histolytica
KeywordsTRANSFERASE / KINASE
Function / homology
Function and homology information


: / adenylyl-sulfate kinase / adenylylsulfate kinase activity / sulfate adenylyltransferase (ATP) activity / ATP binding
Similarity search - Function
: / ATP-sulfurylase PUA-like domain / PUA-like domain / : / Adenylyl-sulfate kinase / Adenylylsulphate kinase / PUA-like superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
adenylyl-sulfate kinase
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsHatanaka R / Kishikawa J / Shiba T
Funding support Japan, 3 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24K10217 Japan
Japan Society for the Promotion of Science (JSPS)25K01949 Japan
Japan Society for the Promotion of Science (JSPS)25K02488 Japan
CitationJournal: J Struct Biol X / Year: 2026
Title: Structural insights into interdomain interactions in APS kinase.
Authors: Ryo Hatanaka / Yukiko Ohsumi / Hiroki Matsui / Ayuna Inoguchi / Hina Yuasa / Fumika Mi-Ichi / Jun-Ichi Kishikawa / Tomoo Shiba /
Abstract: The biosynthetic pathway of 3'-phosphoadenosine-5'-phosphosulfate (PAPS) is a universal and essential metabolic process in many organisms, providing the activated sulfate donor required for the ...The biosynthetic pathway of 3'-phosphoadenosine-5'-phosphosulfate (PAPS) is a universal and essential metabolic process in many organisms, providing the activated sulfate donor required for the synthesis of diverse sulfated metabolites. However, this pathway has undergone substantial evolutionary diversification among species. In , PAPS biosynthesis occurs within the mitosomes, mitochondrion-related organelles (MROs), representing a distinctive example of lineage-specific evolutionary adaptation. PAPS synthesis proceeds through a conserved two-step process, which is sequentially catalyzed by ATP sulfurylase (AS) and adenosine 5'-phosphosulfate (APS) kinase (APSK). In this study, we focused on APSK (APSK). APSK contains an additional AS-like domain (SLD), although its functional role remains unclear. Here, we determined the crystal structure of full-length APSK at 2.60 Å resolution and the structure of the truncated APSK lacking APS kinase domain (KD) (APSK) at 2.10 Å resolution. Structural analyses revealed that the SLD engages in dynamic contacts with the KD. Furthermore, deletion of the domain and mutational analyses indicated that the SLD significantly influences the catalytic activity of the KD. Based on these findings, we propose a new regulatory mechanism in which transient interdomain interactions modulate APS kinase activity, representing an unique evolutionary adaptation of .
History
DepositionMar 31, 2026-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_80056.png

Downloads & links

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Map

FileDownload / File: emd_80056.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 150 pix.
= 202.5 Å		1.35 Å/pix.
x 150 pix.
= 202.5 Å		1.35 Å/pix.
x 150 pix.
= 202.5 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.23
Minimum - Maximum-2.960222 - 3.793299
Average (Standard dev.)0.0009849144 (±0.06935807)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 202.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: 3DVA PC3 start

Fileemd_80056_additional_1.map
Annotation3DVA_PC3_start
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Additional map: 3DVA PC1 start

Fileemd_80056_additional_2.map
Annotation3DVA_PC1_start
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Additional map: 3DVA PC1 last

Fileemd_80056_additional_3.map
Annotation3DVA_PC1_last
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Additional map: 3DVA PC3 last

Fileemd_80056_additional_4.map
Annotation3DVA_PC3_last
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Half map: #1

Fileemd_80056_half_map_1.map
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Half map: #2

Fileemd_80056_half_map_2.map
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Sample components

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Entire : homodimer

EntireName: homodimer
Components
  • Complex: homodimer
    • Protein or peptide: APS kinase Entamoeba histolytica

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Supramolecule #1: homodimer

SupramoleculeName: homodimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Entamoeba histolytica (eukaryote)
Molecular weightTheoretical: 110 KDa

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Macromolecule #1: APS kinase Entamoeba histolytica

MacromoleculeName: APS kinase Entamoeba histolytica / type: protein_or_peptide / ID: 1 / Details: M1-E23 is His-tag and spacer. / Enantiomer: LEVO / EC number: adenylyl-sulfate kinase
Source (natural)Organism: Entamoeba histolytica (eukaryote)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MNHKVHHHHH HIEGRHMELG TLEMATAKIA EAAKFNYPDI TLNSHDMGDF EQMMVNGYAP VNTYMSLKDV QQVISTGHMS NGTIFPKPVV LTLTKQEIKK IEKAKKLALR GPEGTLLGLL TPSEVFELPQ GISNKRRNAT MGITGKLEFV EPPPHYDYTE LRKINKPTNP ...String:
MNHKVHHHHH HIEGRHMELG TLEMATAKIA EAAKFNYPDI TLNSHDMGDF EQMMVNGYAP VNTYMSLKDV QQVISTGHMS NGTIFPKPVV LTLTKQEIKK IEKAKKLALR GPEGTLLGLL TPSEVFELPQ GISNKRRNAT MGITGKLEFV EPPPHYDYTE LRKINKPTNP SIFHGIASPL LKPSIDQLKS LEKDGVKPHI DINVLNIPAP HPLVKTTQKY FKDITVTSHP HDSIKSEDVI LRGIIAKNRG FSHYLVPQCS PKEVSTSLKT IGIKPVVSAT PSYFDKMSSS QLINSIRDGT APNELLSKED LDTFSEIYPP TDKQGLVCFF TGLSGSGKSV VSNAVIERLK QHTNRPIYLL DGDIVRTNLS SELGFSKAHR NINILRIGFV ASLLARSGAI VVCAPIAPYR EIRDEVRKMV SQYGNFVEIH NATPISVCEE RDRKGLYAKA RAGIIKGFTG IDDPYEAPLN PEIYLNTAGK SVDQCANIVI DYLTKKQYIK

UniProtKB: adenylyl-sulfate kinase

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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

Concentration0.24 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMTris-HClTris-HCl
300.0 mMNaClNaCl
1.25 mMATPATP
0.0125 mMAPSAPS
12.5 mMMgCl2MgCl2
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 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

MicroscopeTFS KRIOS
Specialist opticsPhase plate: OTHER / Spherical aberration corrector: corrected / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 11470 / Average exposure time: 3.0 sec. / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.066 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 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: 1923378
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: ab-initio reconstruction
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 450150
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final 3D classificationNumber classes: 4 / Avg.num./class: 125000 / Software - Name: cryoSPARC (ver. 4.4.1)
FSC plot (resolution estimation)

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