7YQ1 | pdb_00007yq1

Crystal structure of adenosine 5'-phosphosulfate kinase from Archaeoglobus fulgidus in complex with AMP-PNP and APS

PDB DOI: https://doi.org/10.2210/pdb7YQ1/pdb

Classification: TRANSFERASE
Organism(s): Archaeoglobus fulgidus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-08-05 Released: 2023-01-18
Deposition Author(s): Kawakami, T., Teramoto, T., Kakuta, Y.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free:
0.246 (Depositor), 0.246 (DCC)
R-Value Work:
0.214 (Depositor), 0.214 (DCC)
R-Value Observed:
0.215 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of adenosine 5'-phosphosulfate kinase isolated from Archaeoglobus fulgidus.

Kawakami, T., Teramoto, T., Kakuta, Y.

(2022) Biochem Biophys Res Commun 643: 105-110

PubMed: 36592583 Search on PubMed
DOI: https://doi.org/10.1016/j.bbrc.2022.12.081
Primary Citation Related Structures:
7YQ0, 7YQ1

PubMed Abstract:
The 3'-phosphoadenosine-5'-phosphosulfate (PAPS) molecule is essential during enzyme-catalyzed sulfation reactions as a sulfate donor and is an intermediate in the reduction of sulfate to sulfite in the sulfur assimilation pathway. PAPS is produced through a two-step reaction involving ATP sulfurylase and adenosine 5'-phosphosulfate (APS) kinase enzymes/domains. However, archaeal APS kinases have not yet been characterized and their mechanism of action remains unclear. Here, we first structurally characterized APS kinase from the hyperthermophilic archaeon Archaeoglobus fulgidus, (AfAPSK). We demonstrated the PAPS production activity of AfAPSK at the optimal growth temperature (83 °C). Furthermore, we determined the two crystal structures of AfAPSK: ADP complex and ATP analog adenylyl-imidodiphosphate (AMP-PNP)/Mg ²⁺/APS complex. Structural and complementary mutational analyses revealed the catalytic and substrate recognition mechanisms of AfAPSK. This study also hints at the molecular basis behind the thermal stability of AfAPSK.

Organizational Affiliation

Laboratory of Biophysical Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan.

Macromolecule Content

Total Structure Weight: 127.05 kDa
Atom Count: 9,849
Modeled Residue Count: 1,037
Deposited Residue Count: 1,050
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylyl-sulfate kinase	A, B, C, D, E A, B, C, D, E, F	175	Archaeoglobus fulgidus	Mutation(s): 0 Gene Names: cysC, XD40_0245, XD48_1780 EC: 2.7.1.25
UniProt
Find proteins for A0A101DF63 (Archaeoglobus fulgidus) Explore A0A101DF63 Go to UniProtKB: A0A101DF63
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A101DF63
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP (Subject of Investigation/LOI) Query on ANP Download:Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain FA [auth F] SDF format, chain H [auth A] SDF format, chain P [auth B] SDF format, chain T [auth C] SDF format, chain X [auth D] MOL2 format, chain BA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain H [auth A] MOL2 format, chain P [auth B] MOL2 format, chain T [auth C] MOL2 format, chain X [auth D] mmCIF format, chain BA [auth E] mmCIF format, chain FA [auth F] mmCIF format, chain H [auth A] mmCIF format, chain P [auth B] mmCIF format, chain T [auth C] mmCIF format, chain X [auth D]	BA [auth E] FA [auth F] H [auth A] P [auth B] T [auth C] BA [auth E], FA [auth F], H [auth A], P [auth B], T [auth C], X [auth D]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain BA [auth E] Focus chain FA [auth F] Focus chain H [auth A] Focus chain P [auth B] Focus chain T [auth C] Focus chain X [auth D] Interactions & Density Focus chain BA [auth E] Focus chain FA [auth F] Focus chain H [auth A] Focus chain P [auth B] Focus chain T [auth C] Focus chain X [auth D]
ADX (Subject of Investigation/LOI) Query on ADX Download:Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain EA [auth F] SDF format, chain G [auth A] SDF format, chain O [auth B] SDF format, chain S [auth C] SDF format, chain W [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain G [auth A] MOL2 format, chain O [auth B] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] mmCIF format, chain AA [auth E] mmCIF format, chain EA [auth F] mmCIF format, chain G [auth A] mmCIF format, chain O [auth B] mmCIF format, chain S [auth C] mmCIF format, chain W [auth D]	AA [auth E] EA [auth F] G [auth A] O [auth B] S [auth C] AA [auth E], EA [auth F], G [auth A], O [auth B], S [auth C], W [auth D]	ADENOSINE-5'-PHOSPHOSULFATE C₁₀ H₁₄ N₅ O₁₀ P S IRLPACMLTUPBCL-KQYNXXCUSA-N		Interactions Focus chain AA [auth E] Focus chain EA [auth F] Focus chain G [auth A] Focus chain O [auth B] Focus chain S [auth C] Focus chain W [auth D] Interactions & Density Focus chain AA [auth E] Focus chain EA [auth F] Focus chain G [auth A] Focus chain O [auth B] Focus chain S [auth C] Focus chain W [auth D]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A]	J [auth A], L [auth A], M [auth A], N [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain J [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A]
BO3 (Subject of Investigation/LOI) Query on BO3 Download:Ideal Coordinates CCD File SDF format, chain DA [auth E] SDF format, chain K [auth A] SDF format, chain R [auth B] SDF format, chain V [auth C] SDF format, chain Z [auth D] SDF format, chain HA [auth F] MOL2 format, chain DA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain R [auth B] MOL2 format, chain V [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain HA [auth F] mmCIF format, chain DA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain R [auth B] mmCIF format, chain V [auth C] mmCIF format, chain Z [auth D] mmCIF format, chain HA [auth F]	DA [auth E] HA [auth F] K [auth A] R [auth B] V [auth C] DA [auth E], HA [auth F], K [auth A], R [auth B], V [auth C], Z [auth D]	BORIC ACID B H₃ O₃ KGBXLFKZBHKPEV-UHFFFAOYSA-N		Interactions Focus chain DA [auth E] Focus chain HA [auth F] Focus chain K [auth A] Focus chain R [auth B] Focus chain V [auth C] Focus chain Z [auth D] Interactions & Density Focus chain DA [auth E] Focus chain HA [auth F] Focus chain K [auth A] Focus chain R [auth B] Focus chain V [auth C] Focus chain Z [auth D]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain GA [auth F] SDF format, chain I [auth A] SDF format, chain Q [auth B] SDF format, chain Y [auth D] SDF format, chain U [auth C] MOL2 format, chain CA [auth E] MOL2 format, chain GA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain Y [auth D] MOL2 format, chain U [auth C] mmCIF format, chain CA [auth E] mmCIF format, chain GA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain Y [auth D] mmCIF format, chain U [auth C]	CA [auth E] GA [auth F] I [auth A] Q [auth B] U [auth C] CA [auth E], GA [auth F], I [auth A], Q [auth B], U [auth C], Y [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth E] Focus chain GA [auth F] Focus chain I [auth A] Focus chain Q [auth B] Focus chain U [auth C] Focus chain Y [auth D] Interactions & Density Focus chain CA [auth E] Focus chain GA [auth F] Focus chain I [auth A] Focus chain Q [auth B] Focus chain U [auth C] Focus chain Y [auth D]