PDBsum entry 1dml

DNA binding protein/transferase

PDB id: 1dml

Contents

Protein chains

267 a.a. *

36 a.a. *

* Residue conservation analysis

PDB id:

1dml

Name:

DNA binding protein/transferase

Title:

Crystal structure of herpes simplex ul42 bound to thE C-terminus of hsv pol

Structure:

DNA polymerase processivity factor. Chain: a, c, e, g. Fragment: n-terminal domain. Synonym: DNA-binding protein ul42. Engineered: yes. DNA polymerase. Chain: b, d, f, h. Fragment: c-terminal 36 amino acids. Engineered: yes

Source:

Human herpesvirus 1. Herpes simplex virus type 1. Organism_taxid: 10298. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.70Å R-factor: 0.230 R-free: 0.281

Authors:

H.J.Zuccola,D.J.Filman,D.M.Coen,J.M.Hogle

Key ref:

H.J.Zuccola et al. (2000). The crystal structure of an unusual processivity factor, herpes simplex virus UL42, bound to the C terminus of its cognate polymerase. Mol Cell, 5, 267-278. PubMed id: 10882068 DOI: 10.1016/S1097-2765(00)80422-0

Date:

14-Dec-99 Release date: 15-Mar-00

Protein chains

P10226  (PAP_HHV11) -  DNA polymerase processivity factor from Human herpesvirus 1 (strain 17)

Seq: 488 a.a.

Struc: 267 a.a.

Protein chains

P07917  (DPOL_HHV1A) -  DNA polymerase catalytic subunit from Human herpesvirus 1 (strain Angelotti)

Seq: 1235 a.a.

Struc: 36 a.a.

Enzyme reactions

• Enzyme class 2: Chains A, C, E, G: E.C.?
• Enzyme class 3: Chains B, D, F, H: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 4: Chains B, D, F, H: E.C.3.1.26.4 - ribonuclease H.
• Reaction: Endonucleolytic cleavage to 5'-phosphomonoester.

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1016/S1097-2765(00)80422-0

Mol Cell 5:267-278 (2000)

PubMed id: 10882068

The crystal structure of an unusual processivity factor, herpes simplex virus UL42, bound to the C terminus of its cognate polymerase.

H.J.Zuccola, D.J.Filman, D.M.Coen, J.M.Hogle.

ABSTRACT

Herpes simplex virus DNA polymerase is a heterodimer composed of a catalytic subunit, Pol, and an unusual processivity subunit, UL42, which, unlike processivity factors such as PCNA, directly binds DNA. The crystal structure of a complex of the C-terminal 36 residues of Pol bound to residues 1-319 of UL42 reveals remarkable similarities between UL42 and PCNA despite contrasting biochemical properties and lack of sequence homology. Moreover, the Pol-UL42 interaction resembles the interaction between the cell cycle regulator p21 and PCNA. The structure and previous data suggest that the UL42 monomer interacts with DNA quite differently than does multimeric toroidal PCNA. The details of the structure lead to a model for the mechanism of UL42, provide the basis for drug design, and allow modeling of other proteins that lack sequence homology with UL42 or PCNA.

Selected figure(s)

Figure 4.
Figure 4. Interaction of the Pol Peptide with UL42The 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.

Figure 7.
Figure 7. Regions of Other Herpesvirus Polymerase Accessory Proteins Predicted to Have PCNA/UL42-like StructuresThe 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.

The above figures are reprinted by permission from Cell Press: Mol Cell (2000, 5, 267-278) copyright 2000.

Figures were selected by an automated process.