PDBsum entry 1xef

Transport protein

PDB id: 1xef

Contents

Protein chains

241 a.a. *

Ligands

ATP ×4

Metals

_MG ×4

Waters ×172

* Residue conservation analysis

PDB id:

1xef

Name:

Transport protein

Title:

Crystal structure of the atp/mg2+ bound composite dimer of hlyb-nbd

Structure:

Alpha-hemolysin translocation atp-binding protein hlyb. Chain: a, b, c, d. Fragment: hlyb-nbd(residues 467-707). Synonym: hlyb. Engineered: yes. Mutation: yes

Source:

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

Biol. unit:

Dimer (from PQS)

Resolution:

2.50Å R-factor: 0.222 R-free: 0.264

Authors:

J.Zaitseva,S.Jenewein,I.B.Holland,L.Schmitt

Key ref:

J.Zaitseva et al. (2005). H662 is the linchpin of ATP hydrolysis in the nucleotide-binding domain of the ABC transporter HlyB. EMBO J, 24, 1901-1910. PubMed id: 15889153 DOI: 10.1038/sj.emboj.7600657

Date:

10-Sep-04 Release date: 07-Jun-05

Protein chains

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

Seq: 707 a.a.

Struc: 241 a.a.*

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

DOI no: 10.1038/sj.emboj.7600657

EMBO J 24:1901-1910 (2005)

PubMed id: 15889153

H662 is the linchpin of ATP hydrolysis in the nucleotide-binding domain of the ABC transporter HlyB.

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

ABSTRACT

The ABC transporter HlyB is a central element of the HlyA secretion machinery, a paradigm of Type I secretion. Here, we describe the crystal structure of the HlyB-NBD (nucleotide-binding domain) with H662 replaced by Ala in complex with ATP/Mg2+. The dimer shows a composite architecture, in which two intact ATP molecules are bound at the interface of the Walker A motif and the C-loop, provided by the two monomers. ATPase measurements confirm that H662 is essential for activity. Based on these data, we propose a model in which E631 and H662, highly conserved among ABC transporters, form a catalytic dyad. Here, H662 acts as a 'linchpin', holding together all required parts of a complicated network of interactions between ATP, water molecules, Mg2+, and amino acids both in cis and trans, necessary for intermonomer communication. Based on biochemical experiments, we discuss the hypothesis that substrate-assisted catalysis, rather than general base catalysis might operate in ABC-ATPases.

Selected figure(s)

Figure 1.
Figure 1 Crystal structure of the HlyB-NBD H662A dimer with bound ATP/Mg2+. ATP in stick representation and Mg2+ (green spheres) are sandwiched at the interface of the two HlyB-NBD monomers (shown in light tan and light yellow). N- and C-termini of the individual monomers are labeled. Conserved motifs are colored in red (Walker A motif; Walker et al, 1982), brown (Q-loop), blue (C-loop or ABC signature motif), magenta (Walker B), black (D-loop), and green (H-loop) and labeled accordingly. The figure was prepared using PyMol (www.pymol.org).

Figure 2.
Figure 2 (A) Stereo view of one of the ATP-binding sites in the HlyB-NBD H662A dimer. ATP is shown in stick representation, Mg2+ as a green sphere, and water molecules as blue spheres. (B) Schematic diagram of the interactions between one of the two ATP/Mg2+ complexes and HlyB-NBD H662A. (C) Schematic diagram of the interactions across the monomer -monomer interface. Color coding is identical to Figure 1. Residues involved in monomer -monomer contact are highlighted by gray boxes, while residues involved in protein -ATP contacts are colored in boxes according to Figure 1. Blue numbers indicate water molecules. Hydrogen bonds and salt bridges are shown as solid lines, while van der Waals and hydrophobic interactions are shown as dashed lines. Letters represent the atoms involved in the interaction.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2005, 24, 1901-1910) copyright 2005.

Figures were selected by an automated process.