PDBsum entry 1im4

Transferase

PDB id: 1im4

Contents

Protein chain

205 a.a. *

Ligands

SO4 ×3

Waters ×110

* Residue conservation analysis

PDB id:

1im4

Name:

Transferase

Title:

Crystal structure of a dinb homolog (dbh) lesion bypass DNA polymerase catalytic fragment from sulfolobus solfataricus

Structure:

Dbh. Chain: a. Fragment: n-terminal catalytic domain (residues 2-216). Synonym: dbh bypass polymerase. Engineered: yes

Source:

Sulfolobus solfataricus. Organism_taxid: 2287. Gene: dbh. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.30Å R-factor: 0.227 R-free: 0.261

Authors:

J.D.Pata,B.L.Zhou,T.A.Steitz

Key ref:

B.L.Zhou et al. (2001). Crystal structure of a DinB lesion bypass DNA polymerase catalytic fragment reveals a classic polymerase catalytic domain. Mol Cell, 8, 427-437. PubMed id: 11545744 DOI: 10.1016/S1097-2765(01)00310-0

Date:

09-May-01 Release date: 12-Sep-01

Protein chain

P96022  (DPO4_SACSO) -  DNA polymerase IV from Saccharolobus solfataricus

Seq: 354 a.a.

Struc: 205 a.a.*

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

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/S1097-2765(01)00310-0

Mol Cell 8:427-437 (2001)

PubMed id: 11545744

Crystal structure of a DinB lesion bypass DNA polymerase catalytic fragment reveals a classic polymerase catalytic domain.

B.L.Zhou, J.D.Pata, T.A.Steitz.

ABSTRACT

The UmuC/DinB family of bypass polymerases is responsible for translesion DNA synthesis and includes the human polymerases eta, iota, and kappa. We determined the 2.3 A resolution crystal structure of a catalytic fragment of the DinB homolog (Dbh) polymerase from Sulfolobus solfataricus and show that it is nonprocessive and can bypass an abasic site. The structure of the catalytic domain is nearly identical to those of most other polymerase families. Homology modeling suggests that there is minimal contact between protein and DNA, that the nascent base pair binding pocket is quite accessible, and that the enzyme is already in a closed conformation characteristic of ternary polymerase complexes. These observations afford insights into the sources of low fidelity and low processivity of the UmuC/DinB polymerases.

Selected figure(s)

Figure 2.
Figure 2. Homology Modeling of DNA from the T7 DNAP Ternary Complex onto the Molecular Surface of Dbh(A) Superposition of the palm domains of Dbh (colored as in Figure 1A) and T7 DNAP (colored in dark gray). The T7 DNAP catalytic aspartates (D475 and D654) and the residues that function as the steric gate (E480) and bind the 3′ terminal phosphorous of the primer strand (H704) are shown in stick representation, as are the corresponding residues from Dbh (D7, D105, F12, and K153). The Mg^2+ ions from the T7 DNAP ternary complex are shown as yellow spheres. Cα atoms used in the superposition were 1–21, 77–95, 97–112, 118–137, and 138–153 from Dbh and 469–487, 614–632, 646–661, 662–681, and 689–704 from T7 DNAP ternary complex (Protein Data Bank code 1T7P; Doublié et al., 1998). Only the structurally aligned core of the palm domains is shown.(B) View looking down onto the Dbh active site. Primer and template DNA (light and dark gray, respectively), incoming nucleotide, and magnesium ions (yellow spheres) from the T7DNAP ternary complex structure (Doublié et al., 1998) were modeled onto the molecular surface of Dbh. Substrate molecules from the T7 DNAP ternary complex structure were positioned onto the Dbh surface based on the superposition of the palm domains shown in (A). The flexible loop and N-terminal His[6]-tag are not shown in surface representation and are, instead, shown with transparent and gray lines, respectively. The molecular surface of Dbh was calculated using a 1.4 Å radius probe in SPOCK (Christopher, 1998) and is colored according to conserved motifs I-V as in Figure 1A.(C) Closer view of the active site with surface colored according to electrostatic potential, with positively charged areas in blue and negatively charged areas in red. The thumb domain has been omitted for clarity, and the molecule has been rotated slightly to show the surface of the nascent base pair binding pocket more clearly. Surface areas contributed by some of the residues discussed in the text are labeled

Figure 3.
Figure 3. Polymerase Active Site of DbhResidues discussed in the text are shown in stick representation together with a ribbons diagram of Dbh. Coloring of conserved motifs is as described in Figure 1A. Hydrogen bonds discussed are indicated with dotted lines

The above figures are reprinted by permission from Cell Press: Mol Cell (2001, 8, 427-437) copyright 2001.

Figures were selected by an automated process.