PDBsum entry 1a5t

Zinc finger

PDB id: 1a5t

Contents

Protein chain

324 a.a. *

Metals

_ZN

Waters ×606

* Residue conservation analysis

PDB id:

1a5t

Name:

Zinc finger

Title:

Crystal structure of the delta prime subunit of the clamp-loader complex of escherichia coli DNA polymerase iii

Structure:

Delta prime. Chain: a. Synonym: holb. Engineered: yes

Source:

Escherichia coli k12. Organism_taxid: 83333. Strain: k-12. Cellular_location: cytoplasm. Gene: holb. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.20Å R-factor: 0.205 R-free: 0.265

Authors:

B.Guenther,R.Onrust,A.Sali,M.O'Donnell,J.Kuriyan

Key ref:

B.Guenther et al. (1997). Crystal structure of the delta' subunit of the clamp-loader complex of E. coli DNA polymerase III. Cell, 91, 335-345. PubMed id: 9363942 DOI: 10.1016/S0092-8674(00)80417-1

Date:

18-Feb-98 Release date: 27-May-98

Protein chain

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

Seq: 334 a.a.

Struc: 324 a.a.

Enzyme reactions

• Enzyme class: 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

DOI no: 10.1016/S0092-8674(00)80417-1

Cell 91:335-345 (1997)

PubMed id: 9363942

Crystal structure of the delta' subunit of the clamp-loader complex of E. coli DNA polymerase III.

B.Guenther, R.Onrust, A.Sali, M.O'Donnell, J.Kuriyan.

ABSTRACT

The crystal structure of the delta' subunit of the clamp-loader complex of E. coli DNA polymerase III has been determined. Three consecutive domains in the structure are arranged in a C-shaped architecture. The N-terminal domain contains a nonfunctional nucleotide binding site. The catalytic component of the clamp-loader complex is the gamma subunit, which is homologous to delta'. A sequence-structure alignment suggests that nucleotides bind to gamma at an interdomain interface within the inner surface of the "C." The alignment is extended to other clamp-loader complexes and to the RuvB family of DNA helicases, and suggests that each of these is assembled from C-shaped components that can open and close the jaws of the "C" in response to ATP binding and hydrolysis.

Selected figure(s)

Figure 5.
Figure 5. Inactive Nucleotide-Binding Region of δ′The region surrounding the P loop of δ′ is shown, with side chains of certain residues indicated in stick representation. P-loop sequences and sensor sequences in δ′ and other proteins are indicated. The structure of ATP is taken from adenylate kinase, after the P-loop segments of adenylate kinase and δ′ were superimposed. Residues that are actual or potential ligands of the phosphate groups of ATP are highlighed in blue in the alignment of sequence motifs.

Figure 6.
Figure 6. GRASP Diagrams of δ′The molecular surface of δ′ is shown in two orientations, colored according to local electrostatic potential. A transparent representation of the surface with the polypeptide backbone revealed underneath is also shown. Note that there are no contacts between Domains 1 and 3, and that the appearance of such contacts in the GRASP diagram is a consequence of the orientation of the molecule. Figure prepared using GRASP ([32]).

The above figures are reprinted by permission from Cell Press: Cell (1997, 91, 335-345) copyright 1997.

Figures were selected by an automated process.