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PDB ID Mentions in PubMed Central Article count: 2

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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

The precatalytic state is represented by structures 4DS6 (3.64 Å resolution [ 29 ]), and 4FAQ (3.11 Å resolution [ 30 ]) – the four-character codes are the Protein Data Bank id... ntifiers.

Under these conditions, the overall intron and the geometry of its active site are not significantly affected (overall RMSD = 0.84 Å between structure 4FAR obtained in the presence of Mg 2+ and structure 4FAQ obtained with Ca 2+ ).

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.

Publication Year: 2013


Evidence for a group II intron-like catalytic triplex in the spliceosome.

(2014) Nat Struct Mol Biol 21

PubMed: 24747940 | PubMedCentral: PMC4257784 | DOI: 10.1038/nsmb.2815

Figure 4 The U6 triplex forms in vitro a, Stacking interaction between C377 and G288, as observed in the group II intron crystal structure (PDB 4FAQ, ref.

Figure 8 The U6 triplex promotes exon ligation in vitro a, Configuration of the C288*C358-G385 base triple in the group II intron (PDB 4FAQ, ref.

c, Structure of the group II intron domain V, highlighting the catalytic triplex (PDB 4FAQ, ref.

Publication Year: 2014