PDBsum entry 3eyc

Transport protein

PDB id: 3eyc

Contents

Protein chain

143 a.a. *

Ligands

BU1 ×4

Waters ×185

* Residue conservation analysis

PDB id:

3eyc

Name:

Transport protein

Title:

New crystal structure of human tear lipocalin in complex with 1,4- butanediol in space group p21

Structure:

Lipocalin-1. Chain: a, b, c, d. Fragment: residues 5-166. Synonym: von ebner gland protein, veg protein, tear prealbumin, tp, tear lipocalin, tlc. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: lcn1. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.60Å R-factor: 0.228 R-free: 0.274

Authors:

D.A.Breustedt,L.Keil,A.Skerra

Key ref:

D.A.Breustedt et al. (2009). A new crystal form of human tear lipocalin reveals high flexibility in the loop region and induced fit in the ligand cavity. Acta Crystallogr D Biol Crystallogr, 65, 1118-1125. PubMed id: 19770509 DOI: 10.1107/S0907444909031011

Date:

20-Oct-08 Release date: 06-Oct-09

Protein chains

P31025  (LCN1_HUMAN) -  Lipocalin-1 from Homo sapiens

Seq: 176 a.a.

Struc: 143 a.a.*

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

DOI no: 10.1107/S0907444909031011

Acta Crystallogr D Biol Crystallogr 65:1118-1125 (2009)

PubMed id: 19770509

A new crystal form of human tear lipocalin reveals high flexibility in the loop region and induced fit in the ligand cavity.

D.A.Breustedt, L.Chatwell, A.Skerra.

ABSTRACT

Tear lipocalin (TLC) with the bound artificial ligand 1,4-butanediol has been crystallized in space group P2(1) with four protein molecules in the asymmetric unit and its X-ray structure has been solved at 2.6 A resolution. TLC is a member of the lipocalin family that binds ligands with diverse chemical structures, such as fatty acids, phospholipids and cholesterol as well as microbial siderophores and the antibiotic rifampin. Previous X-ray structural analysis of apo TLC crystallized in space group C2 revealed a rather large bifurcated ligand pocket and a partially disordered loop region at the entrace to the cavity. Analysis of the P2(1) crystal form uncovered major conformational changes (i) in beta-strands B, C and D, (ii) in loops 1, 2 and 4 at the open end of the beta-barrel and (iii) in the extended C-terminal segment, which is attached to the beta-barrel via a disulfide bridge. The structural comparison indicates high conformational plasticity of the loop region as well as of deeper parts of the ligand pocket, thus allowing adaptation to ligands that differ vastly in size and shape. This illustrates a mechanism for promiscuity in ligand recognition which may also be relevant for some other physiologically important members of the lipocalin protein family.

Selected figure(s)

Figure 3.
Figure 3 Comparison of the TLC structures obtained from two different crystal forms. Molecules were superimposed using the C^ positions of the 58 conserved -barrel residues (as in Fig. 1-b). (a) Superposition of TLC crystallized in space group P2[1] (chain A, blue) and in space group C2 (PDB code 1xki ; gold, with modelled residues in grey; Breustedt et al., 2005[Breustedt, D. A., Korndörfer, I. P., Redl, B. & Skerra, A. (2005). J. Biol. Chem. 280, 484-493.]). The bound 1,4-butanediol and the hydrogen-bonded water molecule are represented as spheres, while the conserved disulfide bond is shown in stick representation (white). Most of the -strands are elongated towards the open end of the -barrel in the P2[1] structure. (b) Pairwise C^ -atom distances between the two different TLC crystal structures after superposition of the 58 conserved C^ positions of the -barrel, resulting in an overall C^ r.m.s.d. value of 1.86 Å ( -strands A-H are labelled as bars; loops 1, 2, 3 and 4 connect strands A and B, C and D, E and F, and G and H, respectively). The largest deviations between the two crystal structures occur in -strands B, C and D and in the neighbouring loops 1 and 2 at the open end of the -barrel. (c) The electrostatic interactions that may trigger the two alternative conformations of loop 1. In the P2[1] structure (dark grey) residues Glu27 and Lys108 (green) at the tips of the adjacent loops 1 and 4 make an electrostatic contact that fixes the `open' conformation of loop 1 (blue). In contrast, the `closed' conformation of this loop in the C2 structure (light grey; loop 1 coloured gold, modelled residues coloured yellow) is stabilized by a similar interaction between residues Glu34 and Lys114 (orange). (d) Flexibility of the region around the disulfide bridge. While the disulfide bond between Cys61 and Cys153 is well ordered in the P2[1] structure (dark grey; loop 2 and the C-terminal peptide segment coloured blue, side chains coloured violet), only residue Cys61 was resolved in the C2 structure (light grey; loop 2 and the C-terminal peptide segment coloured gold, modelled residues coloured yellow, Cys side chain coloured orange) and appears shifted outward by 5.6 Å compared with the P2[1] structure (red dotted line between the corresponding C^ positions). Nevertheless, the C^ distance between Cys61 in the C2 structure and Cys153 in the superimposed P2[1] structure is only 0.3 Å larger than the distance between Cys61 and Cys153 within the P2[1] structure (green dotted lines). By assuming a more extended backbone conformation at residue Glu151 (side chain displayed in blue), the (unresolved) C-terminal peptide segment of the C2 structure could easily span the 0.3 Å distance and move Cys153 sufficiently close to Cys61, indicating that the disulfide bond is probably also formed in the C2 crystal (despite the differing conformation of loop 2) but is not visible in the electron density owing to local structural disorder.

The above figure is reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2009, 65, 1118-1125) copyright 2009.

Figure was selected by the author.