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Now on display: a gallery of group II intron structures at different stages of catalysis.

(2013) Mob DNA 4

PubMed: 23634971 | PubMedCentral: PMC3669008 | DOI: 10.1186/1759-8753-4-14

b PDB entry 3EOG represents the same form of the group II intron in the state preceding the SER reaction as 4E8K, but was solved at a lower resolution (3.39 Å) using construct OiD1-6 [ 31 ].

Table 1 Available 3-D X-ray structures of the group II intron PDB id Resolution (Å) Metals Splicing stage Activity Construct Reference 4DS6 3.64 NH 4 + /Mg 2+ 5′-exon hydrolysis (pre) No (active site mutant) OiD1-6-G359A [ 29 ] 4FAQ 3.11 K + /Ca 2+ 5′-exon hydrolysis (pre) No (nonfunctional divalent ion) Oi5eD1-5 [ 30 ] 4FAR 2.86 K + /Mg 2+ 5′-exon hydrolysis (post) Yes Oi5eD1-5 [ 30 ] 4FAU 2.87 Li + /Mg 2+ Intermediate Partial (nonfunctional monovalent ion) Oi5eD1-5 [ 30 ] 3IGI a 3.13 K + /Mg 2+ Postcatalytic ligand-bound Yes OiD1-6 [ 26 , 27 ] 4E8M 3.50 K + /Mg 2+ Ligand-free Yes OiD1-5 [ 30 ] 4E8P 3.28 Rb + /Mg 2+ Ligand-free Yes OiD1-5 [ 30 ] 4E8R 3.36 Cs + /Mg 2+ Ligand-free Partial (nonfunctional monovalent ion) OiD1-5 [ 30 ] 4E8Q 2.84 Tl + /Mg 2+ Ligand-free Yes OiD1-5 [ 30 ] 4E8N 2.96 NH 4 + /Mg 2+ Ligand-free Yes OiD1-5 [ 30 ] 4E8V 3.99 K + /Ba 2+ Ligand-free No (nonfunctional divalent ion) OiD1-5 [ 30 ] 4FAX 3.10 Na + /Mg 2+ Ligand-free No (nonfunctional monovalent ion) OiD1-5 [ 30 ] 4FB0 3.22 K + /Mg 2+ Ligand-free Partial (active site mutant) OiD1-5-C377G [ 30 ] 4E8K b 3.03 K + /Ca 2+ SER (pre) No (nonfunctional divalent ion) OiD1-5 [ 30 ] 4E8T 3.34 K + /Ca 2+ SER (pre) No (nonfunctional divalent ion) OiD1-5 [ 30 ] 4FAW 2.70 K + /Mg 2+ SER (post) Yes OiD1-5 [ 30 ] a Additional PDB entries 3BWP, 3EOH and 3G78 represent the same form of the group II intron in the state following 3′-exon hydrolysis as 3IGI, which results from the most recent refinement.

By contrast, the structure of the post-hydrolytic state of SER was obtained using the OiD1-5 construct, bound to the same oligonucleotide used for solving 4E8K and 4E8T, but co-crystallized in the presence of physiological ions Mg 2+ and K + (structure 4FAW) [ 30 ].

They are 3EOG (3.39 Å resolution) [ 31 ], 4E8K (3.03 Å resolution) [ 30 ], 4E8T (3.34 Å resolution) [ 30 ], and 4FAW (2.70 Å resolution), respectively [ 30 ].

In another approach to visualizing the precatalytic state of SER, construct OiD1-5 was co-crystallized in the presence of Ca 2+ with an oligonucleotide that corresponds to the sequence of native ligated exons (structures 4E8K and 4E8T) [ 30 ].

Publication Year: 2013