PDBsum entry 2r6f

Hydrolase

PDB id: 2r6f

Contents

Protein chains

899 a.a. *

Ligands

ADP ×4

Metals

_ZN ×6

Waters ×4

* Residue conservation analysis

PDB id:

2r6f

Name:

Hydrolase

Title:

Crystal structure of bacillus stearothermophilus uvra

Structure:

Excinuclease abc subunit a. Chain: a, b. Fragment: uvra. Engineered: yes

Source:

Geobacillus stearothermophilus. Organism_taxid: 272567. Strain: 10. Gene: uvra. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

3.20Å R-factor: 0.257 R-free: 0.292

Authors:

Y.Inuzuka,D.Pakotiprapha,B.R.Bowman,D.Jeruzalmi,G.L.Verdine

Key ref:

D.Pakotiprapha et al. (2008). Crystal Structure of Bacillus stearothermophilus UvrA Provides Insight into ATP-Modulated Dimerization, UvrB Interaction, and DNA Binding. Mol Cell, 29, 122-133. PubMed id: 18158267 DOI: 10.1016/j.molcel.2007.10.026

Date:

05-Sep-07 Release date: 08-Jan-08

Protein chains

Q5KVB6  (Q5KVB6_GEOKA) -  UvrABC system protein A from Geobacillus kaustophilus (strain HTA426)

Seq: 955 a.a.

Struc: 899 a.a.*

* PDB and UniProt seqs differ at 6 residue positions (black crosses)

DOI no: 10.1016/j.molcel.2007.10.026

Mol Cell 29:122-133 (2008)

PubMed id: 18158267

Crystal Structure of Bacillus stearothermophilus UvrA Provides Insight into ATP-Modulated Dimerization, UvrB Interaction, and DNA Binding.

D.Pakotiprapha, Y.Inuzuka, B.R.Bowman, G.F.Moolenaar, N.Goosen, D.Jeruzalmi, G.L.Verdine.

ABSTRACT

The nucleotide excision repair pathway corrects many structurally unrelated DNA lesions. Damage recognition in bacteria is performed by UvrA, a member of the ABC ATPase superfamily whose functional form is a dimer with four nucleotide-binding domains (NBDs), two per protomer. In the 3.2 A structure of UvrA from Bacillus stearothermophilus, we observe that the nucleotide-binding sites are formed in an intramolecular fashion and are not at the dimer interface as is typically found in other ABC ATPases. UvrA also harbors two unique domains; we show that one of these is required for interaction with UvrB, its partner in lesion recognition. In addition, UvrA contains three zinc modules, the number and ligand sphere of which differ from previously published models. Structural analysis, biochemical experiments, surface electrostatics, and sequence conservation form the basis for models of ATP-modulated dimerization, UvrA-UvrB interaction, and DNA binding during the search for lesions.

Selected figure(s)

Figure 2.
Figure 2. Structural Comparison of the NBDs of BstUvrA and Other ABC ATPases
The conserved ATPase motifs are colored as follows: Walker A/P loop, green; Walker B and D loop, orange; ABC signature motif, blue; Q loop, magenta; and H loop/switch, cyan.
(A) Arrangement of the NBDs in E. coli MalK, Pyrococcus furiosus RLI, and BstUvrA. Key residues important for nucleotide binding and interactions across the dimer interface are shown. The transmembrane portion of MalK is depicted in transparent yellow.
(B) NBDs of UvrA were superimposed with the NBDs of the maltose transporter MalK (ADP-bound, PDB code 2AWO; ATP-bound, PDB code 1Q12), and Rad50 (ATP-bound, PDB code 1F2U) using their respective ATP-binding domains. All the motifs are from the same NBD except for the ABC signature motif and the D loop, which are part of the opposing NBD. The bound ADP is from the proximal site of UvrA protomer A and is represented as ball and stick.
(C) Histogram showing the distance between the C[α] atoms of the conserved Lys residue in the Walker A motif and Ser residue in the ABC signature motif in the structures of ABC ATPases solved in the dimeric state (PDB codes 2R6F, 2AWO, 1Q1B, 1Q1E, 2AWN, 1YQT, 1L7V, 2ONK, 1Q12, 1F2U, 1XEF, 1XEX).

Figure 4.
Figure 4. BstUvrA Dimer Interface
C[α] trace of protomers A and B are shown in pale green and pale blue, respectively, with the Zn atoms in gray. The regions involved in polar contacts across the dimer interface are shown using ribbon diagram (green and orange, protomer A; blue and magenta, protomer B). Hydrogen bonds are depicted as dashed lines and the bound ADP molecules as space-filling models. Illustrations in (A) –(C) are shown in the same orientation as in Figure 1B.
(A) UvrA dimer.
(B) Interactions between the Q loop-I and the loop following α helix 1, which contains the Walker A-I motif at its N terminus.
(C) Interactions between the loop preceding Walker B-I and residues of the ATP-binding domain I of the opposing monomer.

The above figures are reprinted from an Open Access publication published by Cell Press: Mol Cell (2008, 29, 122-133) copyright 2008.

Figures were selected by an automated process.