PDBsum entry 1xhz

Transferase/DNA

PDB id: 1xhz

Contents

Protein chains

571 a.a. *

DNA/RNA

Ligands

_DT-_DT

Waters ×512

* Residue conservation analysis

PDB id:

1xhz

Name:

Transferase/DNA

Title:

Phi29 DNA polymerase, orthorhombic crystal form, ssdna complex

Structure:

5'-d( Tp Tp Tp Tp T)-3'. Chain: e, f, g, h. Engineered: yes. DNA polymerase. Chain: a, b, c, d. Synonym: early protein gp2. Engineered: yes. Mutation: yes

Source:

Synthetic: yes. Bacillus phage phi29. Organism_taxid: 10756. Gene: 2. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

2.70Å R-factor: 0.219 R-free: 0.268

Authors:

S.Kamtekar,A.J.Berman,J.Wang,J.M.Lazaro,M.De Vega,L.Blanco,M.Salas, T.A.Steitz

Key ref:

S.Kamtekar et al. (2004). Insights into strand displacement and processivity from the crystal structure of the protein-primed DNA polymerase of bacteriophage phi29. Mol Cell, 16, 609-618. PubMed id: 15546620 DOI: 10.1016/j.molcel.2004.10.019

Date:

21-Sep-04 Release date: 07-Dec-04

Protein chains

P03680  (DPOL_BPPH2) -  DNA polymerase from Bacillus phage phi29

Seq: 575 a.a.

Struc: 571 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DNA/RNA chains

T-T-T-T-T 5 bases

T-T-T-T-T 5 bases

T-T-T-T-T 5 bases

Enzyme reactions

• Enzyme class 2: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 3: E.C.3.1.11.- - ?????

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/j.molcel.2004.10.019

Mol Cell 16:609-618 (2004)

PubMed id: 15546620

Insights into strand displacement and processivity from the crystal structure of the protein-primed DNA polymerase of bacteriophage phi29.

S.Kamtekar, A.J.Berman, J.Wang, J.M.Lázaro, M.de Vega, L.Blanco, M.Salas, T.A.Steitz.

ABSTRACT

The DNA polymerase from phage phi29 is a B family polymerase that initiates replication using a protein as a primer, attaching the first nucleotide of the phage genome to the hydroxyl of a specific serine of the priming protein. The crystal structure of phi29 DNA polymerase determined at 2.2 A resolution provides explanations for its extraordinary processivity and strand displacement activities. Homology modeling suggests that downstream template DNA passes through a tunnel prior to entering the polymerase active site. This tunnel is too small to accommodate double-stranded DNA and requires the separation of template and nontemplate strands. Members of the B family of DNA polymerases that use protein primers contain two sequence insertions: one forms a domain not previously observed in polymerases, while the second resembles the specificity loop of T7 RNA polymerase. The high processivity of phi29 DNA polymerase may be explained by its topological encirclement of both the downstream template and the upstream duplex DNA.

Selected figure(s)

Figure 1.
Figure 1. Ribbon Representation of the Domain Organization of φ29 DNA PolymeraseThe exonuclease domain is shown in red, the palm in pink, TPR1 in gold, the fingers in blue, TPR2 in cyan, and the thumb in green. D249 and D458, which provide the catalytic carboxylates of the polymerase active site, are shown using space-filling spheres.

Figure 4.
Figure 4. Structures of TPR1 and TPR2, Domains that Are Specific to Protein-Primed DNA Polymerases(A) TPR1 forms a compact domain. This region is an insertion between the palm and the fingers subdomains. The motif, identified on the basis of sequence analysis (residues 302–358, gold), can be extended to include residues 261–301 as well (brown), thereby forming a subdomain with no homology to the palm subdomains of other B family polymerases.(B) Structural analogy between TPR2 (cyan) and the specificity loop (gold) of T7 RNA polymerase. The fragments of both palms used for superposition are colored in pink (φ29 DNA polymerase) and gray (T7 RNA polymerase). The atoms of the residues containing the catalytic carboxylates are shown as space-filling spheres.

The above figures are reprinted by permission from Cell Press: Mol Cell (2004, 16, 609-618) copyright 2004.

Figures were selected by an automated process.