8A8H | pdb_00008a8h

APS kinase from Methanothermococcus thermolithotrophicus refined to 1.77 A

PDB DOI: https://doi.org/10.2210/pdb8A8H/pdb

Classification: TRANSFERASE
Organism(s): Methanothermococcus thermolithotrophicus DSM 2095
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-06-23 Released: 2023-04-26
Deposition Author(s): Jespersen, M., Wagner, T.
Funding Organization(s): Max Planck Society, German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free:
0.181 (Depositor), 0.186 (DCC)
R-Value Work:
0.154 (Depositor), 0.161 (DCC)
R-Value Observed:
0.155 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Assimilatory sulfate reduction in the marine methanogen Methanothermococcus thermolithotrophicus.

Jespersen, M., Wagner, T.

(2023) Nat Microbiol 8: 1227-1239

PubMed: 37277534 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41564-023-01398-8
Primary Citation Related Structures:
8A8D, 8A8G, 8A8H, 8A8K, 8A8O

PubMed Abstract:
Methanothermococcus thermolithotrophicus is the only known methanogen that grows on sulfate as its sole sulfur source, uniquely uniting methanogenesis and sulfate reduction. Here we use physiological, biochemical and structural analyses to provide a snapshot of the complete sulfate reduction pathway of this methanogenic archaeon. We find that later steps in this pathway are catalysed by atypical enzymes. PAPS (3'-phosphoadenosine 5'-phosphosulfate) released by APS kinase is converted into sulfite and 3'-phosphoadenosine 5'-phosphate (PAP) by a PAPS reductase that is similar to the APS reductases of dissimilatory sulfate reduction. A non-canonical PAP phosphatase then hydrolyses PAP. Finally, the F ₄₂₀-dependent sulfite reductase converts sulfite to sulfide for cellular assimilation. While metagenomic and metatranscriptomic studies suggest that the sulfate reduction pathway is present in several methanogens, the sulfate assimilation pathway in M. thermolithotrophicus is distinct. We propose that this pathway was 'mix-and-matched' through the acquisition of assimilatory and dissimilatory enzymes from other microorganisms and then repurposed to fill a unique metabolic role.

Organizational Affiliation

Microbial Metabolism Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.

Macromolecule Content

Total Structure Weight: 88.34 kDa
Atom Count: 5,447
Modeled Residue Count: 586
Deposited Residue Count: 768
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
APS kinase from Methanothermococcus thermolithotrophicus	A, B, C, D	192	Methanothermococcus thermolithotrophicus DSM 2095	Mutation(s): 0 Gene Names: cysC EC: 2.7.1.25
UniProt
Find proteins for A0AA82WPC2 (Methanothermococcus thermolithotrophicus DSM 2095) Explore A0AA82WPC2 Go to UniProtKB: A0AA82WPC2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0AA82WPC2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 (Subject of Investigation/LOI) Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain T [auth C] SDF format, chain O [auth B] SDF format, chain J [auth A] SDF format, chain AA [auth D] MOL2 format, chain T [auth C] MOL2 format, chain O [auth B] MOL2 format, chain J [auth A] MOL2 format, chain AA [auth D] mmCIF format, chain T [auth C] mmCIF format, chain O [auth B] mmCIF format, chain J [auth A] mmCIF format, chain AA [auth D]	AA [auth D], J [auth A], O [auth B], T [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain AA [auth D] Focus chain J [auth A] Focus chain O [auth B] Focus chain T [auth C] Interactions & Density Focus chain AA [auth D] Focus chain J [auth A] Focus chain O [auth B] Focus chain T [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain Y [auth D] SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain V [auth D] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain Z [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain V [auth D] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain Z [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain V [auth D] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], L [auth B], M [auth B], N [auth B], Q [auth C], R [auth C], S [auth C], V [auth D], W [auth D], X [auth D], Y [auth D], Z [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain U [auth C] SDF format, chain P [auth B] SDF format, chain K [auth A] SDF format, chain BA [auth D] MOL2 format, chain U [auth C] MOL2 format, chain P [auth B] MOL2 format, chain K [auth A] MOL2 format, chain BA [auth D] mmCIF format, chain U [auth C] mmCIF format, chain P [auth B] mmCIF format, chain K [auth A] mmCIF format, chain BA [auth D]	BA [auth D], K [auth A], P [auth B], U [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BA [auth D] Focus chain K [auth A] Focus chain P [auth B] Focus chain U [auth C] Interactions & Density Focus chain BA [auth D] Focus chain K [auth A] Focus chain P [auth B] Focus chain U [auth C]