6L18

XFEL structure of T4dCH D179N mutant complex with natively expressed dTMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.169 

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Literature

A host dTMP-bound structure of T4 phage dCMP hydroxymethylase mutant using an X-ray free electron laser.

Park, S.H.Park, J.Lee, S.J.Yang, W.S.Park, S.Kim, K.Park, Z.Y.Song, H.K.

(2019) Sci Rep 9: 16316-16316

  • DOI: 10.1038/s41598-019-52825-y
  • Primary Citation of Related Structures:  
    6L18

  • PubMed Abstract: 
  • The hydroxymethylation of cytosine bases plays a vital role in the phage DNA protection system inside the host Escherichia coli. This modification is known to be catalyzed by the dCMP hydroxymethylase from bacteriophage T4 (T4dCH); structural information on the complexes with the substrate, dCMP and the co-factor, tetrahydrofolate is currently available ...

    The hydroxymethylation of cytosine bases plays a vital role in the phage DNA protection system inside the host Escherichia coli. This modification is known to be catalyzed by the dCMP hydroxymethylase from bacteriophage T4 (T4dCH); structural information on the complexes with the substrate, dCMP and the co-factor, tetrahydrofolate is currently available. However, the detailed mechanism has not been understood clearly owing to a lack of structure in the complex with a reaction intermediate. We have applied the X-ray free electron laser (XFEL) technique to determine a high-resolution structure of a T4dCH D179N active site mutant. The XFEL structure was determined at room temperature and exhibited several unique features in comparison with previously determined structures. Unexpectedly, we observed a bulky electron density at the active site of the mutant that originated from the physiological host (i.e., E. coli). Mass-spectrometric analysis and a cautious interpretation of an electron density map indicated that it was a dTMP molecule. The bound dTMP mimicked the methylene intermediate from dCMP to 5'-hydroxymethy-dCMP, and a critical water molecule for the final hydroxylation was convincingly identified. Therefore, this study provides information that contributes to the understanding of hydroxymethylation.


    Organizational Affiliation

    Department of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, South Korea. hksong@korea.ac.kr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Deoxycytidylate 5-hydroxymethyltransferaseA256Escherichia virus T4Mutation(s): 1 
Gene Names: 42
EC: 2.1.2.8
UniProt
Find proteins for P08773 (Enterobacteria phage T4)
Explore P08773 
Go to UniProtKB:  P08773
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08773
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TMP (Subject of Investigation/LOI)
Query on TMP

Download Ideal Coordinates CCD File 
B [auth A]THYMIDINE-5'-PHOSPHATE
C10 H15 N2 O8 P
GYOZYWVXFNDGLU-XLPZGREQSA-N
 Ligand Interaction
IOD
Query on IOD

Download Ideal Coordinates CCD File 
C [auth A]IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.169 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.86α = 90
b = 74.97β = 90
c = 157.62γ = 90
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
CrystFELdata scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

  • Deposited Date: 2019-09-27 
  • Released Date: 2019-12-04 
  • Deposition Author(s): Park, S.H., Song, H.K.

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-04
    Type: Initial release