PDBsum entry 1lrh

Protein binding

PDB id: 1lrh

Contents

Protein chains

160 a.a. *

Ligands

NAG-NAG-BMA-MAN-MAN-MAN ×4

NLA ×4

Metals

_ZN ×4

Waters ×375

* Residue conservation analysis

PDB id:

1lrh

Name:

Protein binding

Title:

Crystal structure of auxin-binding protein 1 in complex with 1- naphthalene acetic acid

Structure:

Auxin-binding protein 1. Chain: a, b, c, d. Engineered: yes. Mutation: yes

Source:

Zea mays. Organism_taxid: 4577. Gene: abp1. Expressed in: trichoplusia ni. Expression_system_taxid: 7111. Expression_system_cell_line: high five.

Biol. unit:

Dimer (from PQS)

Resolution:

1.90Å R-factor: 0.200 R-free: 0.240

Authors:

E.J.Woo,J.Marshall,J.Bauly,J.-G.Chen,M.Venis,R.M.Napier, R.W.Pickersgill

Key ref:

E.J.Woo et al. (2002). Crystal structure of auxin-binding protein 1 in complex with auxin. EMBO J, 21, 2877-2885. PubMed id: 12065401 DOI: 10.1093/emboj/cdf291

Date:

15-May-02 Release date: 19-Jun-02

Protein chains

P13689  (ABP1_MAIZE) -  Auxin-binding protein 1 from Zea mays

Seq: 201 a.a.

Struc: 160 a.a.

DOI no: 10.1093/emboj/cdf291

EMBO J 21:2877-2885 (2002)

PubMed id: 12065401

Crystal structure of auxin-binding protein 1 in complex with auxin.

E.J.Woo, J.Marshall, J.Bauly, J.G.Chen, M.Venis, R.M.Napier, R.W.Pickersgill.

ABSTRACT

The structure of auxin-binding protein 1 (ABP1) from maize has been determined at 1.9 A resolution, revealing its auxin-binding site. The structure confirms that ABP1 belongs to the ancient and functionally diverse germin/seed storage 7S protein superfamily. The binding pocket of ABP1 is predominantly hydrophobic with a metal ion deep inside the pocket coordinated by three histidines and a glutamate. Auxin binds within this pocket, with its carboxylate binding the zinc and its aromatic ring binding hydrophobic residues including Trp151. There is a single disulfide between Cys2 and Cys155. No conformational rearrangement of ABP1 was observed when auxin bound to the protein in the crystal, but examination of the structure reveals a possible mechanism of signal transduction.

Selected figure(s)

Figure 2.
Figure 2 The subunit structure and binding site of ABP1. (A) The -strands of the ABP1 subunit are labelled A'−K; the dimer interface is formed by strands ABIDG and the outer sheet by strands KJCHEF. This figure shows the disulfide between residues 2 and 155 that links the N- and C-terminal extensions; the sulfur atoms are the yellow spheres. Also shown is the relationship between the disulfide, the C-terminal -helix, Trp151 (drawn as ball-and-stick model), 1-NAA (also ball and stick) and the zinc ion (dark blue sphere). The subunit is viewed from the direction of the opening to the auxin-binding pocket. (B) The zinc-binding site in detail. The protein ligands are His57 (strand C), His59 (at the end of strand C), Glu63 (at the beginning of strand D) and His106 (at the beginning of strand H). A single water molecule completes the octahedral coordination sphere. The zinc−nitrogen (His NE2) distances are between 2.2 and 2.3 Å and the zinc−oxygen distances are 2.4 Å to Glu63 OE1, 3.1 Å to Glu63 OE2 and 2.2 Å to the water molecule (shown as a small red sphere).

Figure 3.
Figure 3 Auxin binding to ABP1. (A) Omit electron density map at 1.9 Å resolution and contoured at 3 revealing 1-NAA bound to ABP1. The view in (B) is rotated 60° around the x-axis compared with the view in (A), and His57, Glu63, Leu25 and Ile48 are omitted from this view for clarity. The bidentate binding of the 1-NAA carboxylate to the zinc (dark blue sphere) can be clearly seen, as can the hydrophobic environment of the naphthalene ring. (C) Simplified representation of the contacts between 1-NAA and ABP1 and between the zinc ion and ABP1 in the complex. Distances shown are in angstroms. (A) and (B) were prepared using BOBSCRIPT (Esnouf, 1997).

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2002, 21, 2877-2885) copyright 2002.

Figures were selected by an automated process.