PDBsum entry 2py5

Replication, transferase/DNA

PDB id: 2py5

Contents

Protein chains

564 a.a. *

DNA/RNA

Ligands

EDO ×27

Waters ×1493

* Residue conservation analysis

PDB id:

2py5

Name:

Replication, transferase/DNA

Title:

Phi29 DNA polymerase complexed with single-stranded DNA

Structure:

5'-d(ggacttt)-3'. Chain: j, y, d, e, l. Engineered: yes. DNA polymerase. Chain: a, b. Synonym: early protein gp2. Engineered: yes. Mutation: yes

Source:

Synthetic: yes. Bacillus phage phi29. Organism_taxid: 10756. Gene: 2, gp2. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.60Å R-factor: 0.165 R-free: 0.194

Authors:

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

Key ref:

A.J.Berman et al. (2007). Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases. EMBO J, 26, 3494-3505. PubMed id: 17611604 DOI: 10.1038/sj.emboj.7601780

Date:

15-May-07 Release date: 17-Jul-07

Protein chains

P03680  (DPOL_BPPH2) -  DNA polymerase from Bacillus phage phi29

Seq: 575 a.a.

Struc: 564 a.a.*

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

DNA/RNA chains

G-A-C-T-T-T 6 bases

G-G-A-C-T-T 6 bases

G-G-A-C-T-T 6 bases

G-G-A-C-T-T 6 bases

C-T-T-T 4 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: 10.1038/sj.emboj.7601780

EMBO J 26:3494-3505 (2007)

PubMed id: 17611604

Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases.

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

ABSTRACT

Replicative DNA polymerases (DNAPs) move along template DNA in a processive manner. The structural basis of the mechanism of translocation has been better studied in the A-family of polymerases than in the B-family of replicative polymerases. To address this issue, we have determined the X-ray crystal structures of phi29 DNAP, a member of the protein-primed subgroup of the B-family of polymerases, complexed with primer-template DNA in the presence or absence of the incoming nucleoside triphosphate, the pre- and post-translocated states, respectively. Comparison of these structures reveals a mechanism of translocation that appears to be facilitated by the coordinated movement of two conserved tyrosine residues into the insertion site. This differs from the mechanism employed by the A-family polymerases, in which a conserved tyrosine moves into the templating and insertion sites during the translocation step. Polymerases from the two families also interact with downstream single-stranded template DNA in very different ways.

Selected figure(s)

Figure 3.
Figure 3 Water-mediated interactions maintain sequence nonspecific binding. The C:G base pair is from the ternary1 complex, and the A:T base pair is from the ternary2 complex. Red spheres are water molecules and black dashes are hydrogen bonds. Amino acids are colored by subdomain as in Kamtekar et al (2004).

Figure 4.
Figure 4 The I/YxGG/A motif. (A) The primer and template strands from the ternary complex are shown as yellow and gray sticks, respectively. The template strand and the residues of the I/YxGG/A motif are shown as spheres. (B) The two distinct populations of Y226 are shown in sticks based on a superposition of the palm subdomain. The residues are colored by crystal structure.

The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2007, 26, 3494-3505) copyright 2007.

Figures were selected by an automated process.