7R3A

Crystal structure of S-adenosyl-L-homocysteine hydrolase from Methanococcus maripaludis in complex with inosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure, function and substrate preferences of archaeal S-adenosyl-L-homocysteine hydrolases.

Koeppl, L.H.Popadic, D.Saleem-Batcha, R.Germer, P.Andexer, J.N.

(2024) Commun Biol 7: 380-380

  • DOI: https://doi.org/10.1038/s42003-024-06078-9
  • Primary Citation of Related Structures:  
    7R37, 7R38, 7R39, 7R3A, 8COD, 8QNO

  • PubMed Abstract: 

    S-Adenosyl-L-homocysteine hydrolase (SAHH) reversibly cleaves S-adenosyl-L-homocysteine, the product of S-adenosyl-L-methionine-dependent methylation reactions. The conversion of S-adenosyl-L-homocysteine into adenosine and L-homocysteine plays an important role in the regulation of the methyl cycle. An alternative metabolic route for S-adenosyl-L-methionine regeneration in the extremophiles Methanocaldococcus jannaschii and Thermotoga maritima has been identified, featuring the deamination of S-adenosyl-L-homocysteine to S-inosyl-L-homocysteine. Herein, we report the structural characterisation of different archaeal SAHHs together with a biochemical analysis of various SAHHs from all three domains of life. Homologues deriving from the Euryarchaeota phylum show a higher conversion rate with S-inosyl-L-homocysteine compared to S-adenosyl-L-homocysteine. Crystal structures of SAHH originating from Pyrococcus furiosus in complex with SLH and inosine as ligands, show architectural flexibility in the active site and offer deeper insights into the binding mode of hypoxanthine-containing substrates. Altogether, the findings of our study support the understanding of an alternative metabolic route for S-adenosyl-L-methionine and offer insights into the evolutionary progression and diversification of SAHHs involved in methyl and purine salvage pathways.


  • Organizational Affiliation

    Institute of Pharmaceutical Sciences, University of Freiburg, Albertstr. 25, 79104, Freiburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
S-inosyl-L-homocysteine hydrolase
A, B, C, D, E
A, B, C, D, E, F, G, H
435Methanococcus maripaludisMutation(s): 0 
Gene Names: ahcYMMP0920
EC: 3.13.1.9
UniProt
Find proteins for Q6LYR8 (Methanococcus maripaludis (strain DSM 14266 / JCM 13030 / NBRC 101832 / S2 / LL))
Explore Q6LYR8 
Go to UniProtKB:  Q6LYR8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6LYR8
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD (Subject of Investigation/LOI)
Query on NAD

Download Ideal Coordinates CCD File 
CA [auth G]
FA [auth H]
J [auth A]
M [auth B]
P [auth C]
CA [auth G],
FA [auth H],
J [auth A],
M [auth B],
P [auth C],
S [auth D],
W [auth E],
Z [auth F]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
NOS (Subject of Investigation/LOI)
Query on NOS

Download Ideal Coordinates CCD File 
BA [auth G]
EA [auth H]
I [auth A]
L [auth B]
O [auth C]
BA [auth G],
EA [auth H],
I [auth A],
L [auth B],
O [auth C],
R [auth D],
V [auth E],
Y [auth F]
INOSINE
C10 H12 N4 O5
UGQMRVRMYYASKQ-KQYNXXCUSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
AA [auth G]
DA [auth H]
K [auth A]
N [auth B]
Q [auth C]
AA [auth G],
DA [auth H],
K [auth A],
N [auth B],
Q [auth C],
T [auth D],
U [auth E],
X [auth F]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.775α = 90
b = 328.867β = 107.23
c = 85.094γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany235777276/RTG1976
European Research Council (ERC)GermanyERC project 716966

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-15
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-09-18
    Changes: Database references