The Crystal Structure of an Unusual Processivity Factor, Herpes Simplex Virus UL42, Bound to the C Terminus of Its Cognate Polymerase  Harmon J Zuccola, David J Filman, Donald M Coen, James M Hogle  Molecular Cell  Volume 5, Issue 2, Pages 267-278 (February 2000) DOI: 10.1016/S1097-2765(00)80422-0

Figure 1 Stereo Representation of the Final Atomic Model Superimposed upon a Portion of the Final 2.7 Å Resolution 2FO − FC Electron Density Map Calculated Using CNS The map is contoured at 1σ above the mean electron density and shows residues of both UL42 and the peptide. Molecular Cell 2000 5, 267-278DOI: (10.1016/S1097-2765(00)80422-0)

Figure 2 Comparison of the Structures of UL42 and PCNA A ribbon diagram of UL42 ([A] and [B]; blue) shows that its overall fold is almost identical to that of human PCNA ([C] and [D]; red; PDB accession number 1AXC). The numbering of the strands and helices in UL42 is the same nomenclature used for human PCNA (Gulbis et al. 1996). The blue italicized αB1 indicates a loop of UL42 that is helical in PCNA. The loop between the βD1 and βE1 strands is found in two different conformations. In one case, the loop is extended, and in the other case, the loop is folded back under the βD1 and βE1 strands. (A and C) Front views of UL42 and PCNA, respectively. (B and D) Side views of UL42 and PCNA, respectively. (E and F) Backbone trace showing the superposition of UL42 onto PCNA. Using 90 alpha carbon positions in the C-terminal domain for the superposition, the overall rmsd between the two domains is 1.9 Å. The N-terminal domain of UL42 is rotated approximately 30° about the long axis of the molecule relative to the first domain of PCNA. (This figure was produced using MOLSCRIPT). Molecular Cell 2000 5, 267-278DOI: (10.1016/S1097-2765(00)80422-0)

Figure 3 Implications for DNA Binding Based upon the Electrostatic Surface of UL42 GRASP electrostatic surfaces for PCNA (A) and UL42 (B). Red represents negatively charged surface, blue postive, and white neutral. The left panel shows the front of the molecules in the same orientation as in Figure 2A, and the right panel shows the back surface of the molecules. Both molecules have been contoured at ±10kT/e−. (C) Model of the complex between HSV Pol, UL42, and DNA based upon the recent model of the RB69 Pol bound to DNA and gp45 (Shamoo and Steitz 1999) and the crystal structure of T. gorgonarius Pol (Hopfner et al. 1999). The UL42 electrostatic surface representation is colored as described above, the HSV Pol molecular surface is in white, the missing 22 residues unaccounted for before the beginning of peptide A (see Experimental Procedures) are shown as a ribbon in cyan, peptide A ribbon is colored yellow, and the DNA, which is in one of several possible orientations tethered by the positively charged surface of UL42, is represented as a ribbon in red. Molecular Cell 2000 5, 267-278DOI: (10.1016/S1097-2765(00)80422-0)

Figure 4 Interaction of the Pol Peptide with UL42 The peptide is folded into an αβα structure on the front surface of UL42. (A) Ribbon diagram of UL42 (blue) bound to peptide A (orange) (UL42 is oriented as in Figure 2). (B) Molecular surface representation of UL42 with peptide A bound. P1 and P2 denote pockets formed on the surface of the molecule. Labeled residues belong to the peptide, except for that of UL42 Q171, which is labeled as a projection on the surface. The side chains of the peptide are colored as follows: blue, K, R, and H; red, D and E; yellow, G; magenta, A; cyan, T; and white, L, V, and F. (C) Schematic representation of the intermolecular hydrogen bonds between the peptide (orange) and UL42 (blue). Spheres represent the alpha carbons. The cylinders represent the two helices of the peptide, and the arrows indicate the region of Pol and UL42 that form the antiparallel β strands. Molecular Cell 2000 5, 267-278DOI: (10.1016/S1097-2765(00)80422-0)

Figure 5 Stereo Representation of the Locations of UL42 Linker Insertion Mutants and Potential DNA-Binding Sites UL42 (blue), peptide (orange), and phosphate backbone of the DNA (magenta) are shown as coils. The α-carbon positions of the linker insertion mutants are shown in black, and the positions of the potential DNA-binding residues (R113, R182, R279, R280, and Q282) are shown in red. The side chains of these residues and those of the hydrophobic core of the C-terminal domain are shown as ball-and-stick models and colored according to element (C, green, O, red, N, blue, and S, yellow). I-160 exhibits impaired Pol binding; I-203 and I-206 exhibit impaired DNA binding. Molecular Cell 2000 5, 267-278DOI: (10.1016/S1097-2765(00)80422-0)

Figure 6 Comparison of UL42/Peptide A Complex with that of the Other Sliding Clamp Processivity Factors PCNA (red)/p21 (yellow), UL42 (blue)/Pol (orange), and gp45 (green)/RB69 peptide (yellow). Molecular Cell 2000 5, 267-278DOI: (10.1016/S1097-2765(00)80422-0)

Figure 7 Regions of Other Herpesvirus Polymerase Accessory Proteins Predicted to Have PCNA/UL42-like Structures The UCLA-DOE fold recognition server at http://fold.doe-mbi.ucla.edu was sent the sequences of human cytomegalovirus (HCMV) UL44, human herpesvirus-6 (HHV-6) p41, Kaposi sarcoma–associated herpesvirus (human herpesvirus-8, HHV-8) PF-8, and Epstein-Barr virus (EBV) BMRF1. HCMV and HHV-6 are β herpesviruses, and EBV and HHV-8 are γ herpesviruses. Molecular Cell 2000 5, 267-278DOI: (10.1016/S1097-2765(00)80422-0)