PDBsum entry: 1egi

Sugar binding protein

PDB id: 1egi

Contents

Protein chains

129 a.a. *

143 a.a. *

Metals

_CA ×3

Waters ×115

* Residue conservation analysis

PDB id:

1egi

Name:

Sugar binding protein

Title:

Structure of a c-type carbohydrate-recognition domain (crd- 4) from the macrophage mannose receptor

Structure:

Macrophage mannose receptor. Chain: a, b. Fragment: carbohydrate-recognition domain 4. Engineered: yes

Source:

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

Biol. unit:

Dimer (from PQS)

Resolution:

2.30Å R-factor: 0.212 R-free: 0.262

Authors:

H.Feinberg,S.Park-Snyder,A.R.Kolatkar,C.T.Heise,M.E.Taylor, W.I.Weis

Key ref:

H.Feinberg et al. (2000). Structure of a C-type carbohydrate recognition domain from the macrophage mannose receptor. J Biol Chem, 275, 21539-21548. PubMed id: 10779515 DOI: 10.1074/jbc.M002366200

Date:

15-Feb-00 Release date: 30-Aug-00

Protein chain

P22897  (MRC1_HUMAN) -  Macrophage mannose receptor 1

Seq: 1456 a.a.

Struc: 129 a.a.

Protein chain

P22897  (MRC1_HUMAN) -  Macrophage mannose receptor 1

Seq: 1456 a.a.

Struc: 143 a.a.*

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

 Gene Ontology (GO) functional annotation 

• Biochemical function: binding (1 term)

DOI no: 10.1074/jbc.M002366200

J Biol Chem 275:21539-21548 (2000)

PubMed id: 10779515

Structure of a C-type carbohydrate recognition domain from the macrophage mannose receptor.

H.Feinberg, S.Park-Snyder, A.R.Kolatkar, C.T.Heise, M.E.Taylor, W.I.Weis.

ABSTRACT

The mannose receptor of macrophages and liver endothelium mediates clearance of pathogenic organisms and potentially harmful glycoconjugates. The extracellular portion of the receptor includes eight C-type carbohydrate recognition domains (CRDs), of which one, CRD-4, shows detectable binding to monosaccharide ligands. We have determined the crystal structure of CRD-4. Although the basic C-type lectin fold is preserved, a loop extends away from the core of the domain to form a domain-swapped dimer in the crystal. Of the two Ca(2+) sites, only the principal site known to mediate carbohydrate binding in other C-type lectins is occupied. This site is altered in a way that makes sugar binding impossible in the mode observed in other C-type lectins. The structure is likely to represent an endosomal form of the domain formed when Ca(2+) is lost from the auxiliary calcium site. The structure suggests a mechanism for endosomal ligand release in which the auxiliary calcium site serves as a pH sensor. Acid pH-induced removal of this Ca(2+) results in conformational rearrangements of the receptor, rendering it unable to bind carbohydrate ligands.

Selected figure(s)

Figure 3.
Fig. 3. Flexibility of the extended loop region. The CRD cores of the two independent copies of mannose receptor CRD-4 ( brown, copy A; blue, copy B) have been superimposed along with the cores of the two subunits of the IX/X-BP (yellow and cyan).

Figure 5.
Fig. 5. Comparison of Ca^2+ binding in the principal site between mannose receptor CRD-4 (gray bonds), MBP-A (brown bonds), and E-selectin (yellow bonds). Red, blue, and green spheres represent oxygen, nitrogen, and calcium, respectively. Ca^2+ coordination bonds are shown as dashed lines and hydrogen bonds are shown as thin solid lines. In CRD-4, residues 725, 727, and 728 come from one protomer of the dimer, and 747 and 748 come from the other protomer. In A, and B, the residue numbers are from the mannose receptor, with the equivalent MBP-A (A) or E-selectin (B) residue numbers shown in parentheses. In C, MBP-A numbers are shown with equivalent residue numbers of E-selectin shown in parentheses.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2000, 275, 21539-21548) copyright 2000.

Figures were selected by an automated process.