PDBsum entry 3glg

Transferase/DNA

PDB id: 3glg

Contents

Protein chains

333 a.a. *

(+ 0 more) 364 a.a. *

334 a.a. *

DNA/RNA

Ligands

ADP-BEF ×5

ADP

BEF

Metals

_ZN ×8

_MG ×6

* Residue conservation analysis

PDB id:

3glg

Name:

Transferase/DNA

Title:

Crystal structure of a mutant (gammat157a) e. Coli clamp loader bound to primer-template DNA

Structure:

DNA polymerase iii subunit delta. Chain: a, f. Engineered: yes. DNA polymerase iii subunit tau. Chain: b, c, d, g, h, i. Fragment: unp residues 1-373. Synonym: DNA polymerase iii subunit gamma. Engineered: yes. Mutation: yes.

Source:

Escherichia coli. Organism_taxid: 83333. Strain: k-12. Gene: hola, b0640, jw0635. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: dnax, dnaz, dnazx, b0470, jw0459. Gene: holb, b1099, jw1085. Synthetic: yes.

Resolution:

3.25Å R-factor: 0.226 R-free: 0.263

Authors:

K.R.Simonetta,S.N.Seyedin,J.Kuriyan

Key ref:

K.R.Simonetta et al. (2009). The mechanism of ATP-dependent primer-template recognition by a clamp loader complex. Cell, 137, 659-671. PubMed id: 19450514

Date:

12-Mar-09 Release date: 26-May-09

Protein chains

P28630  (HOLA_ECOLI) -  DNA polymerase III subunit delta from Escherichia coli (strain K12)

Seq: 343 a.a.

Struc: 333 a.a.

Protein chains

P06710  (DPO3X_ECOLI) -  DNA polymerase III subunit tau from Escherichia coli (strain K12)

Seq: 643 a.a.

Struc: 364 a.a.*

Protein chains

P28631  (HOLB_ECOLI) -  DNA polymerase III subunit delta' from Escherichia coli (strain K12)

Seq: 334 a.a.

Struc: 334 a.a.

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

DNA/RNA chains

T-T-T-T-T-A-T-A-G-G-C-C-A-G 14 bases

C-T-G-G-C-C-T-A-T-A 10 bases

T-T-T-T-T-A-T-A-G-G-C-C-A-G 14 bases

C-T-G-G-C-C-T-A-T-A 10 bases

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, F, G, H, I, J: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate

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

Added reference

Cell 137:659-671 (2009)

PubMed id: 19450514

The mechanism of ATP-dependent primer-template recognition by a clamp loader complex.

K.R.Simonetta, S.L.Kazmirski, E.R.Goedken, A.J.Cantor, B.A.Kelch, R.McNally, S.N.Seyedin, D.L.Makino, M.O'Donnell, J.Kuriyan.

ABSTRACT

Clamp loaders load sliding clamps onto primer-template DNA. The structure of the E. coli clamp loader bound to DNA reveals the formation of an ATP-dependent spiral of ATPase domains that tracks only the template strand, allowing recognition of both RNA and DNA primers. Unlike hexameric helicases, in which DNA translocation requires distinct conformations of the ATPase domains, the clamp loader spiral is symmetric and is set up to trigger release upon DNA recognition. Specificity for primed DNA arises from blockage of the end of the primer and accommodation of the emerging template along a surface groove. A related structure reveals how the psi protein, essential for coupling the clamp loader to single-stranded DNA-binding protein (SSB), binds to the clamp loader. By stabilizing a conformation of the clamp loader that is consistent with the ATPase spiral observed upon DNA binding, psi binding promotes the clamp-loading activity of the complex.