PDBsum entry 2ffb

Transport protein

PDB id: 2ffb

Contents

Protein chain

243 a.a. *

Ligands

ADP

Waters ×128

* Residue conservation analysis

PDB id:

2ffb

Name:

Transport protein

Title:

The crystal structure of the hlyb-nbd e631q mutant in complex with adp

Structure:

Alpha-hemolysin translocation atp-binding protein hlyb. Chain: a. Fragment: amino acids 467-707. Engineered: yes. Mutation: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: hlyb. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.90Å R-factor: 0.204 R-free: 0.250

Authors:

J.Zaitseva,C.Oswald,T.Jumpertz,S.Jenewein,I.B.Holland,L.Schmitt

Key ref:

J.Zaitseva et al. (2006). A structural analysis of asymmetry required for catalytic activity of an ABC-ATPase domain dimer. EMBO J, 25, 3432-3443. PubMed id: 16858415 DOI: 10.1038/sj.emboj.7601208

Date:

19-Dec-05 Release date: 08-Aug-06

Protein chain

P08716  (HLYBP_ECOLX) -  Alpha-hemolysin translocation ATP-binding protein HlyB from Escherichia coli

Seq: 707 a.a.

Struc: 243 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

DOI no: 10.1038/sj.emboj.7601208

EMBO J 25:3432-3443 (2006)

PubMed id: 16858415

A structural analysis of asymmetry required for catalytic activity of an ABC-ATPase domain dimer.

J.Zaitseva, C.Oswald, T.Jumpertz, S.Jenewein, A.Wiedenmann, I.B.Holland, L.Schmitt.

ABSTRACT

The ATP-binding cassette (ABC)-transporter haemolysin (Hly)B, a central element of a Type I secretion machinery, acts in concert with two additional proteins in Escherichia coli to translocate the toxin HlyA directly from the cytoplasm to the exterior. The basic set of crystal structures necessary to describe the catalytic cycle of the isolated HlyB-NBD (nucleotide-binding domain) has now been completed. This allowed a detailed analysis with respect to hinge regions, functionally important key residues and potential energy storage devices that revealed many novel features. These include a structural asymmetry within the ATP dimer that was significantly enhanced in the presence of Mg2+, indicating a possible functional asymmetry in the form of one open and one closed phosphate exit tunnel. Guided by the structural analysis, we identified two amino acids, closing one tunnel by an apparent salt bridge. Mutation of these residues abolished ATP-dependent cooperativity of the NBDs. The implications of these new findings for the coupling of ATP binding and hydrolysis to functional activity are discussed.

Selected figure(s)

Figure 1.
Figure 1 The catalytic cycle of the HlyB-NBD. Crystal structures of the monomeric nucleotide-free (Schmitt et al, 2003), dimeric ATP-bound (H662A and E631Q) and monomeric ADP-bound (wild type, E631Q and H662A) forms (this study) are shown. For simplicity, the structure of the ATP/Mg^2+-bound form (Zaitseva et al, 2005a) is not shown. The catalytic domain is colored in light yellow and the helical domain in light tan. Conserved motifs are highlighted and color-coded as follows: Walker A (residues 502–510, blue), Q-loop (residues 549–556, brown), ABC-signature motif (residues 606–610, red), Pro-loop (residues 623–625, orange), Walker B (residues 626–630, magenta), D-loop (residues 634–637, black) and H-loop (residues 661–663, green). Bound ligands are shown in ball-and-stick representation. K[D] values were taken from Zaitseva et al (2005b).

Figure 2.
Figure 2 Nucleotide-binding sites. Stereoview of the ATP-binding (A) and ATP/Mg^2+-binding(B) sites. Color-coding is identical to Figure 1. Direct and water-mediated protein–ATP interactions are highlighted in yellow. Water molecules are shown as blue spheres and Mg^2+ as a green sphere. The interaction between D637 of the D-loop of the trans monomer and S504 of the Walker A motif of the cis monomer is indicated. ATP and amino acids involved in ligand interactions are shown in ball-and-stick representation. ^* indicates conserved motifs of the trans monomer participating in ATP coordination. (C) Stereoview of the ADP-binding site. ADP and residues involved in ligand interactions are shown in ball-and-stick representation, water molecules are blue spheres, protein–ADP interactions are highlighted in green and ADP–water interactions in blue. Color-coding is identical to Figure 1. The interaction between the side chain of Q550 and the amide backbone of T633 is highlighted by a dashed, brown line.

The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2006, 25, 3432-3443) copyright 2006.

Figures were selected by the author.