PDBsum entry 1dyk

Metal binding protein

PDB id: 1dyk

Contents

Protein chain

374 a.a. *

Metals

_CA ×2

Waters ×251

* Residue conservation analysis

PDB id:

1dyk

Name:

Metal binding protein

Title:

Laminin alpha 2 chain lg4-5 domain pair

Structure:

Laminin alpha 2 chain. Chain: a. Fragment: laminin g-like domain 4-5 pair. Engineered: yes. Mutation: yes

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Strain: fvb/n. Tissue: embryo. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_cell_line: ebna-293. Expression_system_cell: emryonic kidney cell.

Resolution:

2.00Å R-factor: 0.233 R-free: 0.261

Authors:

D.Tisi,J.F.Talts,R.Timple,E.Hohenester

Key ref:

D.Tisi et al. (2000). Structure of the C-terminal laminin G-like domain pair of the laminin alpha2 chain harbouring binding sites for alpha-dystroglycan and heparin. EMBO J, 19, 1432-1440. PubMed id: 10747011 DOI: 10.1093/emboj/19.7.1432

Date:

01-Feb-00 Release date: 04-Feb-01

Protein chain

Q60675  (LAMA2_MOUSE) -  Laminin subunit alpha-2 from Mus musculus

Seq: 3118 a.a.

Struc: 374 a.a.*

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

DOI no: 10.1093/emboj/19.7.1432

EMBO J 19:1432-1440 (2000)

PubMed id: 10747011

Structure of the C-terminal laminin G-like domain pair of the laminin alpha2 chain harbouring binding sites for alpha-dystroglycan and heparin.

D.Tisi, J.F.Talts, R.Timpl, E.Hohenester.

ABSTRACT

The laminins are large heterotrimeric glycoproteins with fundamental roles in basement membrane architecture and function. The C-terminus of the laminin alpha chain contains a tandem of five laminin G-like (LG) domains. We report the 2.0 A crystal structure of the laminin alpha2 LG4-LG5 domain pair, which harbours binding sites for heparin and the cell surface receptor alpha-dystroglycan, and is 41% identical to the laminin alpha1 E3 fragment. LG4 and LG5 are arranged in a V-shaped fashion related by a 110 degrees rotation about an axis passing near the domain termini. An extended N-terminal segment is disulfide bonded to LG5 and stabilizes the domain pair. Two calcium ions, one each in LG4 and LG5, are located 65 A apart at the tips of the domains opposite the polypeptide termini. An extensive basic surface region between the calcium sites is proposed to bind alpha-dystroglycan and heparin. The LG4-LG5 structure was used to construct a model of the laminin LG1-LG5 tandem and interpret missense mutations underlying protein S deficiency.

Selected figure(s)

Figure 2.
Figure 2 (A) The LG4–LG5 interface. The colour scheme is the same as in Figure 1. Residues involved in inter-domain contacts are shown as ball-and-stick models and are labelled. The most prominent contact is centred on Phe2931 (see the text). (B) Interactions between the N-terminal segment (in brown) and LG5 (in green). Dashed lines indicate hydrogen bonds. The electron density shown is a simulated annealing 2F[obs] - F[calc] omit map at 2.0 Å resolution (1.5 contouring), in which the N-terminal segment and Cys3017 in LG5 were excluded from the phasing model.

Figure 4.
Figure 4 Calcium-binding sites in 2LG4–5. (A) Calcium 1 in LG4. The calcium ligands are shown as ball-and-stick models and are labelled. Calcium–ligand bonds are shown as black sticks. A metal-bound water molecule is shown in yellow. (B) Calcium 2 in LG5. The calcium coordination is similar to calcium 1, but Asp2861 from a packing-related molecule in the crystal (in yellow) occupies the fifth coordination site (see the text).

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2000, 19, 1432-1440) copyright 2000.

Figures were selected by an automated process.