8A8K

PAP phosphatase from Methanothermococcus thermolithotrophicus refined to 3.1 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

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

  • DOI: https://doi.org/10.1038/s41564-023-01398-8
  • Primary Citation of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PAP phosphatase from Methanothermococcus thermolithotrophicus
A, B, C, D, E
A, B, C, D, E, F
335Methanothermococcus thermolithotrophicus DSM 2095Mutation(s): 0 
EC: 3.1.3.7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AMP (Subject of Investigation/LOI)
Query on AMP

Download Ideal Coordinates CCD File 
G [auth A]
I [auth B]
M [auth C]
O [auth D]
Q [auth E]
G [auth A],
I [auth B],
M [auth C],
O [auth D],
Q [auth E],
U [auth F]
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A]
J [auth B]
K [auth B]
L [auth B]
N [auth C]
H [auth A],
J [auth B],
K [auth B],
L [auth B],
N [auth C],
R [auth E],
T [auth F]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN (Subject of Investigation/LOI)
Query on MN

Download Ideal Coordinates CCD File 
P [auth D],
S [auth E],
V [auth F]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 174.054α = 90
b = 174.054β = 90
c = 183.803γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--
German Research Foundation (DFG)GermanyWA 4053/1-1

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-26
    Type: Initial release
  • Version 1.1: 2023-11-15
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-05-01
    Changes: Refinement description