1. Volume 24, Issue 11, Pages 1960-1971 (November 2016)
Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease 
Setsu Nakae, Atsushi Hijikata, Toshiyuki Tsuji, Kouki Yonezawa, Ken-ichi Kouyama, Kouta Mayanagi, Sonoko Ishino, Yoshizumi Ishino, Tsuyoshi Shirai 
Structure 
Volume 24, Issue 11, Pages (November 2016)
DOI: /j.str
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2. Structure 2016 24, 1960-1971DOI: (10.1016/j.str.2016.09.005)
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3. Figure 1 Structure of TkoEndoMS in Complex with Mismatched dsDNA
(A) Model of the TkoEndoMS-dsDNA complex in front (left) and side (right) views. Key residues for catalytic activity (Asp165Ala, Glu179, and Lys181) and mismatch base binding (Tyr41, Asn76, and Trp77) are shown as ball and stick models. Only one of the alternative dsDNA models is shown (see Figure S5G).
(B) Scheme of dsDNA interactions of TkoEndoMS. Hydrogen bonds are shown as blue-dotted lines. Black-dotted lines indicate cleavage positions. Metal ion interactions are shown with red dotted lines. Those through D165A are hypothetical and not observed in the crystal structures because D165 was mutated.
(C) The residues at the catalytic site are shown as ball and stick models. Hydrogen bonds are shown as orange-dotted lines.
(D) The omit (Fo − Fc) map of TkoEndoMS in complex with G-T-mismatch-DNA1 contoured at 5.0 σ is shown on the model. The nucleotides at 5′ and 3′ sides of scissile bond and Mg2+ ion were omitted in map calculation.
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4. Figure 2 Similarity of TkoEndoMS to Restriction Enzyme
(A) Local alignment of the TkoEndoMS active site sequence with those of the type II restriction endonucleases SgrAI (PDB: 3N78A), Bse634I (PDB: 3V21D), and BsoBI (PDB: 1DC1D). Numbers indicate the first and omitted (in parentheses) residues. Blue shading indicates conserved residues.
(B) Quaternary structures of EndoMS (top) and BsoBI (bottom). The corresponding C-terminal catalytic domains (green and pink), N-terminal dimerizing domains (blue and tan), and dsDNA (red and orange) are colored accordingly between two proteins.
(C) Superposition of the catalytic domains of EndoMS (light blue) and BsoBI (sky blue). Conserved catalytic sites, D165A, E179, and K181 (in the numbering system of TkoEndoMS) are shown as ball and stick models.
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5. Figure 3 Mismatch Base Recognition of TkoEndoMS
(A and B) Residues comprising the mismatch base recognition site are shown for (A) crystal structures binding G or T bases (left) and for (B) predicted model structures binding A or C bases (right). Critical hydrogen bonds for base recognition are shown as orange-dotted lines, and critical atoms for base discrimination are indicated with red and blue dotted circles for G or T and A or C, respectively.
(C) A model of dsDNA in B-form (colored in blue and sky; PDB: 1BNA; Drew et al., 1981) was superposed onto the TkoEndoMS-bound dsDNA (red and yellow). The flipped out bases (G8 and T8), and upward (T9-A7) and downward (C7-G9) base pairs were labeled, and increase between base pairs was indicated with an arrow (see Figure S5I for a larger view).
(D) Superposition of TkoEndoMS in apo (colored dim blue and brown) and dsDNA-bound (light blue and light brown) forms. The disordered loops from Glu125 to Glu135 in the apo form are indicated with dotted lines, and the residues in one of the ordered loops in the dsDNA-bound form are shown as a ball-and-stick model (orange). The hydrogen bonds are shown as yellow lines.
(E) Superposition of the apo forms of TkoEndoMS (dim blue and brown) and PabNucS (sky blue and light yellow). The disordered loops are indicated with dotted lines.
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6. Figure 4 Model Structure of TkoEndoMS-TkoPCNA-DNA Complex
(A) Top and side views of the complex model. The key residues in the PIP box are shown as a ball and stick model (magenta). Possible PIP box positions on remaining PIP-binding sites are shown in pink.
(B) Close-up view of the PIP-binding site. The residues common between EndoMS (light blue) and RFCL (green) are shown in magenta and shaded in the local alignment below.
(C) Model projections and class averages of the TkoEndoMS-TkoPCNA-dsDNA complex. Corresponding model images (top) and their projections (middle) are compared with class averages (bottom) in each column.
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7. Figure 5
Structures of G-T Mismatch-Binding Enzymes and EndoMS Interactions
(A) G-T mismatch recognition structures of Vsr (top, PDB: 1CW0), MBD4 (middle, PDB: 4E9G), and TkoEndoMS (bottom). The flipped out bases in MBD4 (single) and EndoMS (double) are indicated by arrows in the close-up views shown on left. Entire structures are shown on right with DNA bending angle.
(B) The relationships between EndoMS and other proteins detected or predicted with multiple methods. The physical contacts were detected through pull-down assays (solid line), small-angle X-ray scattering (SAXS, thick solid line), or electron microscopy (EM, thick solid line). The functional relationships were predicted through gene co-occurrence (dotted line) or operon structures (double line).
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8. Figure 6
Knowledge-Based Modeling of the TkoEndoMS-dsDNA Search Model and the TkoEndoMS-TkoPCNA-DNA Complex Model
Modeling processes of N- (NTD) and C-terminal (CTD) domain dimers for molecular replacement are schematically presented on the left side. Subunits are differently colored for PabNucS and BsoBI. The scheme on the right side shows the modeling processes of the TkoEndoMS-TkoPCNA-dsDNA complex. Subunits are differently colored for each model.
Structure  , DOI: ( /j.str )
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