We apologize for Proteopedia being slow to respond. For the past two years, a new implementation of Proteopedia has been being built. Soon, it will replace this 18-year old system. All existing content will be moved to the new system at a date that will be announced here.

6l18

From Proteopedia

Jump to: navigation, search

XFEL structure of T4dCH D179N mutant complex with natively expressed dTMP

Structural highlights

6l18 is a 1 chain structure with sequence from Escherichia virus T4. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.9Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DCHM_BPT4

Publication Abstract from PubMed

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.

A host dTMP-bound structure of T4 phage dCMP hydroxymethylase mutant using an X-ray free electron laser.,Park SH, Park J, Lee SJ, Yang WS, Park S, Kim K, Park ZY, Song HK Sci Rep. 2019 Nov 8;9(1):16316. doi: 10.1038/s41598-019-52825-y. PMID:31705139^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Park SH, Park J, Lee SJ, Yang WS, Park S, Kim K, Park ZY, Song HK. A host dTMP-bound structure of T4 phage dCMP hydroxymethylase mutant using an X-ray free electron laser. Sci Rep. 2019 Nov 8;9(1):16316. doi: 10.1038/s41598-019-52825-y. PMID:31705139 doi:http://dx.doi.org/10.1038/s41598-019-52825-y