[English] 日本語
Yorodumi
- PDB-23vk: Crystal structure of full-length of APS kinase from Entamoeba his... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 23vk
TitleCrystal structure of full-length of APS kinase from Entamoeba histolytica
Componentsadenylyl-sulfate kinase
KeywordsTRANSFERASE / KINASE / sulfate activation
Function / homology
Function and homology information


: / : / adenylyl-sulfate kinase / adenylylsulfate kinase activity / sulfate adenylyltransferase (ATP) activity / ATP binding / cytoplasm
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.595 Å
AuthorsHatanaka, R. / Yuasa, H. / Inoguchi, A. / Matsui, H. / Osumi, Y. / Mi-ichi, F. / Kishikawa, J. / Shiba, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)Grant-in-Aid for Scientific Research(B), 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
DepositionFeb 20, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2026Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: adenylyl-sulfate kinase
B: adenylyl-sulfate kinase
C: adenylyl-sulfate kinase
D: adenylyl-sulfate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,8368
Polymers222,4514
Non-polymers3844
Water23413
1
A: adenylyl-sulfate kinase
B: adenylyl-sulfate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,4184
Polymers111,2262
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-46 kcal/mol
Surface area40510 Å2
MethodPISA
2
C: adenylyl-sulfate kinase
D: adenylyl-sulfate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,4184
Polymers111,2262
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-45 kcal/mol
Surface area40220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.449, 158.387, 226.163
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11D-602-

HOH

-
Components

#1: Protein
adenylyl-sulfate kinase


Mass: 55612.859 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: CL6EHI_179080 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5K1U9J0, adenylyl-sulfate kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10 mM Tris-HCl (pH 8.0) 100 mM NaCl 1 mM TCEP 5 mM APS 5 mM AMP-PNP 5 mM MgCl2 0.24 M K2SO4 16% PEG3400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 28, 2023
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 79795 / % possible obs: 99.5 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Net I/σ(I): 14.36
Reflection shellResolution: 2.59→2.75 Å / Mean I/σ(I) obs: 0.8 / Num. unique obs: 12586 / CC1/2: 0.531

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
XDSdata scaling
CRANK2phasing
BUCCANEERmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.595→19.97 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / Cross valid method: FREE R-VALUE / ESU R: 0.513 / ESU R Free: 0.303
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2648 3995 5.019 %
Rwork0.2265 75601 -
all0.228 --
obs-79596 99.308 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 111.398 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2---0.001 Å2-0 Å2
3---0.001 Å2
Refinement stepCycle: LAST / Resolution: 2.595→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14065 0 20 13 14098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01214376
X-RAY DIFFRACTIONr_bond_other_d0.0010.01614028
X-RAY DIFFRACTIONr_angle_refined_deg1.2851.82419499
X-RAY DIFFRACTIONr_angle_other_deg0.7691.76132523
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.89951798
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.572564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.224102584
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.51510572
X-RAY DIFFRACTIONr_chiral_restr0.070.22259
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216289
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022943
X-RAY DIFFRACTIONr_nbd_refined0.2210.23009
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2140.213060
X-RAY DIFFRACTIONr_nbtor_refined0.1750.27091
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.27552
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2315
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1140.227
X-RAY DIFFRACTIONr_nbd_other0.2370.2117
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1180.27
X-RAY DIFFRACTIONr_mcbond_it7.38810.9147216
X-RAY DIFFRACTIONr_mcbond_other7.38710.9147216
X-RAY DIFFRACTIONr_mcangle_it11.33719.6229006
X-RAY DIFFRACTIONr_mcangle_other11.33619.6229007
X-RAY DIFFRACTIONr_scbond_it7.56211.4277160
X-RAY DIFFRACTIONr_scbond_other7.5511.4317145
X-RAY DIFFRACTIONr_scangle_it11.81220.80710493
X-RAY DIFFRACTIONr_scangle_other11.79820.81510470
X-RAY DIFFRACTIONr_lrange_it15.98104.34715515
X-RAY DIFFRACTIONr_lrange_other15.981104.34715516
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.595-2.6620.4882680.49553220.49557840.8490.85796.64590.531
2.662-2.7330.4832760.4653540.46156330.8620.87899.94670.484
2.733-2.8110.4812820.4551950.45154800.8770.87899.94530.461
2.811-2.8960.4282690.40450480.40553180.8880.90199.98120.399
2.896-2.9880.3733020.33948610.34151650.9110.92599.96130.321
2.988-3.0910.392290.31447790.31750160.8910.93199.84050.298
3.091-3.2050.3412540.29645740.29848320.9210.94299.91720.281
3.205-3.3320.3672480.30644430.3146960.9160.93999.89350.294
3.332-3.4760.3282120.29342610.29444910.9310.9599.59920.279
3.476-3.640.3272060.27440650.27642780.9280.95899.83640.26
3.64-3.8290.2811900.26139410.26241350.9480.96299.90330.248
3.829-4.0520.2992020.24236580.24538700.9460.96599.74160.234
4.052-4.320.2521950.20534890.20836890.9620.97599.86450.202
4.32-4.6480.2161820.17932660.18134540.9720.9899.82630.183
4.648-5.0640.2181680.18130010.18331770.9710.97999.74820.19
5.064-5.6170.2771340.19227860.19529280.9570.97999.72680.202
5.617-6.4020.2531180.20124740.20326040.9620.97899.53920.215
6.402-7.6460.2361210.19521390.19722760.9670.97799.2970.215
7.646-10.0990.186820.14717380.14918330.9770.98799.29080.179
10.099-19.970.139570.18412070.18212790.9890.97998.82720.228

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more