8A8K | pdb_00008a8k

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 (Depositor), 0.196 (DCC) 
  • R-Value Work: 
    0.186 (Depositor) 
  • R-Value Observed: 
    0.187 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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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 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: 230.9 kDa 
  • Atom Count: 15,417 
  • Modeled Residue Count: 1,898 
  • Deposited Residue Count: 2,010 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
UniProt
Find proteins for A0AA82WPC3 (Methanothermococcus thermolithotrophicus DSM 2095)
Explore A0AA82WPC3 
Go to UniProtKB:  A0AA82WPC3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AA82WPC3
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 (Depositor), 0.196 (DCC) 
  • R-Value Work:  0.186 (Depositor) 
  • R-Value Observed: 0.187 (Depositor) 
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

View Full Validation Report



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