7EEW

Crystal structure of the intact MTase from Vibrio vulnificus YJ016 in complex with the DNA-mimicking Ocr protein and the S-adenosyl-L-homocysteine (SAH)

Summary for 7EEW

• Entry DOI: 10.2210/pdb7eew/pdb
• Descriptor: Type I restriction-modification system methyltransferase subunit, Overcome classical restriction gp0.3, S-ADENOSYL-L-HOMOCYSTEINE, ... (4 entities in total)
• Functional Keywords: type i restriction-modification system, methyltransferase, ocr, transferase
• Biological source: Vibrio vulnificus (strain YJ016); More
• Total number of polymer chains: 2
• Total formula weight: 86074.27

Authors

Seo, P.W.,Park, S.Y.,Kim, J.S. (deposition date: 2021-03-19, release date: 2022-03-23, Last modification date: 2024-05-29)

Primary citation

Seo, P.W.,Hofmann, A.,Kim, J.H.,Hwangbo, S.A.,Kim, J.H.,Kim, J.W.,Huynh, T.Y.L.,Choy, H.E.,Kim, S.J.,Lee, J.,Lee, J.O.,Jin, K.S.,Park, S.Y.,Kim, J.S.
Structural features of a minimal intact methyltransferase of a type I restriction-modification system.
Int.J.Biol.Macromol., 208:381-389, 2022

PubMed Abstract: Type I restriction-modification enzymes are oligomeric proteins composed of methylation (M), DNA sequence-recognition (S), and restriction (R) subunits. The different bipartite DNA sequences of 2-4 consecutive bases are recognized by two discerned target recognition domains (TRDs) located at the two-helix bundle of the two conserved regions (CRs). Two M-subunits and a single S-subunit form an oligomeric protein that functions as a methyltransferase (MS MTase). Here, we present the crystal structure of the intact MTase from Vibrio vulnificus YJ016 in complex with the DNA-mimicking Ocr protein and the S-adenosyl-L-homocysteine (SAH). This MTase includes the M-domain with a helix tail (M-tail helix) and the S-domain of a TRD and a CR α-helix. The Ocr binds to the cleft of the TRD surface and SAH is located in the pocket within the M-domain. The solution- and negative-staining electron microscopy-based reconstructed (MS) structure reveals a symmetric (S) assembly using two CR-helices and two M-tail helices as a pivot, which is plausible for recognizing two DNA regions of same sequence. The conformational flexibility of the minimal MS MTase dimer indicates a particular state resembling the structure of MS MTases.

PubMed: 35337914
DOI: 10.1016/j.ijbiomac.2022.03.115

Experimental method

X-RAY DIFFRACTION (2.896 Å)