1. Last Stop on the Road to Repair: Structure of E
Last Stop on the Road to Repair: Structure of E. coli DNA Ligase Bound to Nicked DNA- Adenylate 
Jayakrishnan Nandakumar, Pravin A. Nair, Stewart Shuman 
Molecular Cell 
Volume 26, Issue 2, Pages (April 2007)
DOI: /j.molcel
Copyright © 2007 Elsevier Inc. Terms and Conditions

2. Figure 1 Comparison of the EcoLigA and Human Lig1 DNA Clamps
(A) Ribbon diagrams are shown of the structures EcoLigA (left) and human Lig1 (right, PDB 1X9N). The proteins were superimposed with respect to their NTase domains (colored cyan), which concomitantly aligned their respective OB domains (colored magenta). DNA is omitted from the central cavity to highlight the intradomain contacts that “close” the clamp (indicated by red arrows). In EcoLigA, the NTase and HhH (beige) domains make kissing contacts. In contrast, LigI closes its clamp via contacts between the N-terminal DNA binding domain (DBD, in beige) and the C-terminal OB domain (magenta). The terminal domains are indicated by N and C, respectively.
(B) Space-filling models of the EcoLigA and human Lig1 protein are shown with DNA in the cavity. The view is looking down the helical axis, similar to the orientation in (A).
(C) Stereo view of the clamp-closing contacts between amino acids in the NTase (cyan) and HhH (beige) domains of EcoLigA. The interactions occur within the DNA major groove opposite the nick, which has undergone step 2 catalysis to form the AppDNA intermediate.
Molecular Cell  , DOI: ( /j.molcel )
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3. Figure 2 DNA Interface of the HhH Domain
(A) Ribbon diagram of the EcoLigA HhH domain bound to nicked duplex DNA, which is shown as a semitransparent surface. The four “loop-helix” motifs that bind the backbone across the minor groove are indicated by asterisks (∗).
(B) Detailed views of each of the four loop helices bound to their respective 5′-NpNpN target sites. The amino acid sequences are indicated with a dot above the conserved glycines. Protein contacts to the DNA are indicated by dashed lines. Waters are shown as red spheres.
(C) The two (HhH)2 modules of the HhH domain were superimposed and then offset laterally. The terminal residues of the modules are indicated.
Molecular Cell  , DOI: ( /j.molcel )
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4. Figure 3 DNA Interface of the OB Domain
Stereo views of the OB domain (magenta) and Zn-finger domain (green) of EcoLigA (shown as ribbon traces) bound to the nicked DNA, which is rendered as a transparent surface over a stick model.
(A) This view highlights the tetracysteine zinc coordination complex, which is remote from the DNA, and the concave DNA binding surface of the OB β barrel, which makes numerous contacts with the backbone of the template DNA strand, as shown.
(B) This view illustrates the penetration of the OB domain into the minor grove opposite the adenylylated nick (App). The proximity of the nick 3′O to the nick 5′ phosphorus (3.2 Å) is denoted by the magenta dashed line. Val383 and Ile384 contact and splay apart the terminal base pairs at the nick.
Molecular Cell  , DOI: ( /j.molcel )
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5. Figure 4 The Nucleotidyltransferase Domain
Stereo views of the NTase domain (shown as a cyan ribbon trace) bound to the nick, which is rendered as a transparent surface over a stick model.
(A) This view highlights the cage of β strand surrounding the nick 5′ adenylate (at top right) and the numerous interactions of the helix that inserts into the minor groove.
(B) This view illustrates the penetration of the Arg208 into the minor groove and the contacts of motif Ia (135TRG137) to the phosphates of the 3′-OH strand.
Molecular Cell  , DOI: ( /j.molcel )
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6. Figure 5
Architecture of the LigA Active Site for Phosphodiester Synthesis
(A) Stereo view of the interactions at the adenylylated nick. Waters are depicted as red spheres. The water proposed to mimic the divalent cation cofactor for step 3 catalysis is indicated by an asterisk (∗).
(B) Stereo view of the electron density from a composite simulated annealing omit map contoured at 1 σ and shown in mesh representation overlying a stick model of the nick and Lys115.
Molecular Cell  , DOI: ( /j.molcel )
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7. Figure 6
Protein Domain Movements Drive Progression through the Ligation Pathway
(A) Aligned structures of EfaLigA bound to NAD+ (top left, PDB 1TAE), EfaLigA bound to NMN and sulfate (top right, PDB 1TA8), the covalent TfiLigA-AMP intermediate (lower left, PDB 1V9P), and the EcoLigA-AppDNA intermediate (lower right). The structures were superimposed with respect to their NTase domains (cyan) to reveal the large movements of the Ia domain (blue) as the ligase proceeds down the reaction pathway.
(B) The structures of TfiLigA-AMP (left) and EcoLigA-AppDNA (right) were superimposed with respect to their NTase domains (cyan) to reveal the large movements of the OB (magenta), Zn-finger (green), and HhH (beige) domains as a consequence of DNA binding.
Molecular Cell  , DOI: ( /j.molcel )
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8. Figure 7
Remodeling of Adenosine Contacts during Catalysis and Identification of a Structural Target for Inhibitor Design
(A–C) The aligned active sites of the EfaLigA-NAD+ complex (A), the TfiLigA-AMP covalent intermediate (B), and the EcoLigA-AppDNA intermediate (C) highlight the conformational switches of the adenosine nucleoside from syn (A) to anti (B) and then back to syn (C) as the reaction proceeds. The contacts of key active site residues (identified by EcoLigA numbering in [C]) are remodeled at serial steps of the reaction.
(D) An opaque surface view of EcoLigA-AppDNA complex looking into the hydrophobic tunnel of the NTase domain that leads from the surface to the back end of the adenosine binding pocket. The hydrophobic residues lining the tunnel are indicated. The C2 atom of adenine is pointing into the tunnel. The DNA is at lower left.
Molecular Cell  , DOI: ( /j.molcel )
Copyright © 2007 Elsevier Inc. Terms and Conditions