PDBsum entry 5e4k

Sugar binding protein

PDB id: 5e4k

Contents

Protein chain

424 a.a.

Ligands

NAG ×2

1PE

PE5

Metals

_CA ×2

_NA

Waters ×26

PDB id:

5e4k

Name:

Sugar binding protein

Title:

Structure of ligand binding region of uparap at ph 7.4

Structure:

C-type mannose receptor 2. Chain: a. Fragment: ligand binding region, unp residues 31-510. Synonym: uparap. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: mrc2, clec13e, endo180, kiaa0709, uparap. Expressed in: drosophila melanogaster. Expression_system_taxid: 7227.

Resolution:

2.58Å R-factor: 0.217 R-free: 0.257

Authors:

C.Yuan,M.Huang

Key ref:

C.Yuan et al. (2016). Crystal structures of the ligand-binding region of uPARAP: effect of calcium ion binding. Biochem J, 473, 2359-2368. PubMed id: 27247422 DOI: 10.1042/BCJ20160276

Date:

06-Oct-15 Release date: 10-Aug-16

Protein chain

Q9UBG0  (MRC2_HUMAN) -  C-type mannose receptor 2 from Homo sapiens

Seq: 1479 a.a.

Struc: 424 a.a.*

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

DOI no: 10.1042/BCJ20160276

Biochem J 473:2359-2368 (2016)

PubMed id: 27247422

Crystal structures of the ligand-binding region of uPARAP: effect of calcium ion binding.

C.Yuan, H.J.Jürgensen, L.H.Engelholm, R.Li, M.Liu, L.Jiang, Z.Luo, N.Behrendt, M.Huang.

ABSTRACT

The proteins of the mannose receptor (MR) family share a common domain organization and have a broad range of biological functions. Urokinase plasminogen activator receptor-associated protein (uPARAP) (or Endo180) is a member of this family and plays an important role in extracellular matrix remodelling through interaction with its ligands, including collagens and urokinase plasminogen activator receptor (uPAR). We report the crystal structures of the first four domains of uPARAP (also named the ligand-binding region, LBR) at pH 7.4 in Ca(2+)-bound and Ca(2+)-free forms. The first domain (cysteine-rich or CysR domain) folds into a new and unique conformation different from the β-trefoil fold of typical CysR domains. The so-called long loop regions (LLRs) of the C-type lectin-like domain (CTLD) 1 and 2 (the third and fourth domain) mediate the direct contacts between these domains. These LLRs undergo a Ca(2+)-dependent conformational change, and this is likely to be the key structural determinant affecting the overall conformation of uPARAP. Our results provide a molecular mechanism to support the structural flexibility of uPARAP, and shed light on the structural flexibility of other members of the MR family.