6LTV

Crystal Structure of I122A/I330A variant of S-adenosylmethionine synthetase from Cryptosporidium hominis in complex with ONB-SAM (2-nitro benzyme S-adenosyl-methionine)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Engineered SAM Synthetases for Enzymatic Generation of AdoMet Analogs with Photocaging Groups and Reversible DNA Modification in Cascade Reactions.

Michailidou, F.Klocker, N.Cornelissen, N.V.Singh, R.K.Peters, A.Ovcharenko, A.Kummel, D.Rentmeister, A.

(2021) Angew Chem Int Ed Engl 60: 480-485

  • DOI: https://doi.org/10.1002/anie.202012623
  • Primary Citation of Related Structures:  
    6LTV, 6LTW

  • PubMed Abstract: 

    Methylation and demethylation of DNA, RNA and proteins has emerged as a major regulatory mechanism. Studying the function of these modifications would benefit from tools for their site-specific inhibition and timed removal. S-Adenosyl-L-methionine (AdoMet) analogs in combination with methyltransferases (MTases) have proven useful to map or block and release MTase target sites, however their enzymatic generation has been limited to aliphatic groups at the sulfur atom. We engineered a SAM synthetase from Cryptosporidium hominis (PC-ChMAT) for efficient generation of AdoMet analogs with photocaging groups that are not accepted by any WT MAT reported to date. The crystal structure of PC-ChMAT at 1.87 Å revealed how the photocaged AdoMet analog is accommodated and guided engineering of a thermostable MAT from Methanocaldococcus jannaschii. PC-MATs were compatible with DNA- and RNA-MTases, enabling sequence-specific modification ("writing") of plasmid DNA and light-triggered removal ("erasing").


  • Organizational Affiliation

    Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
S-adenosylmethionine synthase
A, B
414Cryptosporidium hominisMutation(s): 2 
Gene Names: CHUDEA7_2650
EC: 2.5.1.6
UniProt
Find proteins for A0A0S4TKQ5 (Cryptosporidium hominis)
Explore A0A0S4TKQ5 
Go to UniProtKB:  A0A0S4TKQ5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0S4TKQ5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EU9 (Subject of Investigation/LOI)
Query on EU9

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[(3R)-3-azanyl-4-oxidanyl-4-oxidanylidene-butyl]-[(2-nitrophenyl)methyl]sulfanium
C21 H26 N7 O7 S
UTGYKEAAXXLVQJ-OUPAZNFWSA-O
3PO (Subject of Investigation/LOI)
Query on 3PO

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
TRIPHOSPHATE
H5 O10 P3
UNXRWKVEANCORM-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.169α = 90
b = 100.167β = 95.99
c = 66.945γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyKU2531/2

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-21
    Type: Initial release
  • Version 1.1: 2021-01-06
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Refinement description