5ZMM

Structure of the Type IV phosphorothioation-dependent restriction endonuclease ScoMcrA

Summary for 5ZMM

• Entry DOI: 10.2210/pdb5zmm/pdb
• Descriptor: Uncharacterized protein McrA, ZINC ION, SULFATE ION, ... (4 entities in total)
• Functional Keywords: type iv restriction endonuclease, dna phosphorothioation, dna binding protein
• Biological source: Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)
• Total number of polymer chains: 6
• Total formula weight: 374512.72

Authors

Liu, G.,Fu, W.,Zhang, Z.,He, Y.,Yu, H.,Zhao, Y.,Deng, Z.,Wu, G.,He, X. (deposition date: 2018-04-04, release date: 2018-09-26, Last modification date: 2024-03-27)

Primary citation

Liu, G.,Fu, W.,Zhang, Z.,He, Y.,Yu, H.,Wang, Y.,Wang, X.,Zhao, Y.,Deng, Z.,Wu, G.,He, X.
Structural basis for the recognition of sulfur in phosphorothioated DNA.
Nat Commun, 9:4689-4689, 2018

PubMed Abstract: There have been very few reports on protein domains that specifically recognize sulfur. Here we present the crystal structure of the sulfur-binding domain (SBD) from the DNA phosphorothioation (PT)-dependent restriction endonuclease ScoMcrA. SBD contains a hydrophobic surface cavity that is formed by the aromatic ring of Y164, the pyrolidine ring of P165, and the non-polar side chains of four other residues that serve as lid, base, and wall of the cavity. The SBD and PT-DNA undergo conformational changes upon binding. The SRGRR loop inserts into the DNA major groove to make contacts with the bases of the GGCC core sequence. Mutating key residues of SBD impairs PT-DNA association. More than 1000 sequenced microbial species from fourteen phyla contain SBD homologs. We show that three of these homologs bind PT-DNA in vitro and restrict PT-DNA gene transfer in vivo. These results show that SBD-like PT-DNA readers exist widely in prokaryotes.

PubMed: 30409991
DOI: 10.1038/s41467-018-07093-1

Experimental method

X-RAY DIFFRACTION (3.15 Å)