PDBsum entry 1yyp

Replication/transferase

PDB id: 1yyp

Contents

Protein chains

249 a.a. *

20 a.a. *

Ligands

SO4 ×4

EDO ×3

Waters ×48

* Residue conservation analysis

PDB id:

1yyp

Name:

Replication/transferase

Title:

Crystal structure of cytomegalovirus ul44 bound to c-terminal peptide from cmv ul54

Structure:

DNA polymerase processivity factor. Chain: a. Fragment: n-terminal domain. Synonym: polymerase accessory protein, pap, icp36 protein. Engineered: yes. DNA polymerase. Chain: b. Fragment: c-terminal 22 residues. Synonym: pol.

Source:

Human herpesvirus 5. Human cytomegalovirus. Organism_taxid: 10359. Gene: ul44. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes

Biol. unit:

Dimer (from PDB file)

Resolution:

2.50Å R-factor: 0.197 R-free: 0.227

Authors:

B.A.Appleton,J.Brooks,A.Loregian,D.J.Filman,D.M.Coen,J.M.Hogle

Key ref:

B.A.Appleton et al. (2006). Crystal structure of the cytomegalovirus DNA polymerase subunit UL44 in complex with the C terminus from the catalytic subunit. Differences in structure and function relative to unliganded UL44. J Biol Chem, 281, 5224-5232. PubMed id: 16371349 DOI: 10.1074/jbc.M506900200

Date:

25-Feb-05 Release date: 27-Dec-05

Protein chain

P16790  (VPAP_HCMVA) -  DNA polymerase processivity factor from Human cytomegalovirus (strain AD169)

Seq: 433 a.a.

Struc: 249 a.a.*

Protein chain

P08546  (DPOL_HCMVA) -  DNA polymerase catalytic subunit from Human cytomegalovirus (strain AD169)

Seq: 1242 a.a.

Struc: 20 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class 2: Chain A: E.C.?
• Enzyme class 3: Chain B: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate

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: 10.1074/jbc.M506900200

J Biol Chem 281:5224-5232 (2006)

PubMed id: 16371349

Crystal structure of the cytomegalovirus DNA polymerase subunit UL44 in complex with the C terminus from the catalytic subunit. Differences in structure and function relative to unliganded UL44.

B.A.Appleton, J.Brooks, A.Loregian, D.J.Filman, D.M.Coen, J.M.Hogle.

ABSTRACT

The human cytomegalovirus DNA polymerase is composed of a catalytic subunit, UL54, and an accessory protein, UL44, which has a structural fold similar to that of other processivity factors, including herpes simplex virus UL42 and homotrimeric sliding clamps such as proliferating cell nuclear antigen. Several specific residues in the C-terminal region of UL54 and in the "connector loop" of UL44 are required for the association of these proteins. Here, we describe the crystal structure of residues 1-290 of UL44 in complex with a peptide from the extreme C terminus of UL54, which explains this interaction at a molecular level. The UL54 peptide binds to structural elements similar to those used by UL42 and the sliding clamps to associate with their respective binding partners. However, the details of the interaction differ from those of other processivity factor-peptide complexes. Crucial residues include a three-residue hydrophobic "plug" from the UL54 peptide and Ile(135) of UL44, which forms a critical intramolecular hydrophobic anchor for interactions between the connector loop and the peptide. As was the case for the unliganded UL44 structure, the UL44-peptide complex forms a head-to-head dimer that could potentially form a C-shaped clamp on DNA. However, the peptide-bound structure displays subtle differences in the relative orientation of the two subdomains of the protein, resulting in a more open clamp, which we predicted would affect its association with DNA. Indeed, filter binding assays revealed that peptide-bound UL44 binds DNA with higher affinity. Thus, interaction with the catalytic subunit appears to affect both the structure and function of UL44.

Selected figure(s)

Figure 2.
FIGURE 2. Molecular details of the UL44-UL54 interface. A, the connector loop of UL44 (white) and the UL54 peptide (brown) are joined by an extensive network of hydrogen bonds (green dots). Four intermolecular hydrogen bonds are formed between main chain atoms of the connector loop (residues 133-137) and the peptide (residues 1234-1238). Additional hydrogen bonds are observed between the side chain of Gln^133 (yellow) of UL44 and the main chain of the peptide and between the side chains of Gln^51 and Lys^60 (light blue) of UL44 and the main chain of the connector loop. Ile^135 (yellow) of UL44 forms a critical hydrophobic anchor below the hydrogen-bonding network. For clarity, only the side chains of Gln^51, Lys^60, Gln^133, and Ile^135 are shown. B, Leu^1227, Phe^1231, and Tyr^1234 (magenta) are part of a hydrophobic plug that packs against a hydrophobic crevice composed of Val^136 (yellow) from the connector loop (cyan) as well as hydrophobic and aliphatic side chains (green) from the central -sheet of UL44. C, the molecular surface of UL44 reveals pockets that accommodate the three-residue hydrophobic plug of UL54.

Figure 3.
FIGURE 3. Comparison of the processivity factor-peptide structures of HSV UL42, HCMV UL44, and human PCNA. A, the association of HSV UL42 (Protein Data Bank code 1DML) with the UL30 peptide (orange) is primarily stabilized by interactions between the C-terminal helix of the peptide and a groove on the left side of the connector loop (red in each panel). His^1228 and Arg^1229 from the C-terminal helix of the peptide are hydrogenbonded to Arg^64 and Gln^171, respectively, of UL42. B, in contrast, the HCMV UL54 peptide (blue) makes significant interactions with UL44 on the right side of the connector loop. This interaction depends largely on three hydrophobic residues from the peptide that bind to a hydrophobic crevice on UL44. The side chains of Leu^1227 and Phe^1231 of UL54 are required for the association with UL44. Although the HSV UL30 peptide has an aromatic residue (Phe^1211) that packs into an analogous crevice on UL42 (see inset in A), this interaction is not essential. C, like UL44, PCNA (Protein Data Bank code 1AXC [PDB] ) contains a hydrophobic crevice on the right side of the connector loop that binds to a peptide from its respective binding partner, p21^WAF1/CIP1 (green). Similar to the UL54 peptide, the p21^WAF1/CIP1 peptide buries three hydrophobic residues in the crevice. The connector loop from each processivity factor forms an antiparallel -sheet with its respective peptide. In each inset, the processivity factor is gray; the connector loop is red; and the peptide backbone is tan.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 5224-5232) copyright 2006.

Figures were selected by an automated process.