PDBsum entry: 1fih

Sugar binding protein

PDB-id: 1fih

Biological unit* = asymmetric unit,
as shown
(*as deduced by PQS)

Contents

Description

Header details

Header records

References

PROCHECK

Protein chains

154 a.a. *

Ligands

NGA ×4

Metal ions

_CL ×3

_CA ×9

Waters ×171

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

1fih

Name:

Sugar binding protein

Title:

N-acetylgalactosamine binding mutant of mannose-binding protein a (qpdwg-hdrpy), complex with n-acetylgalactosamine

Structure:

Mannose-binding protein a. Chain: a, b, c. Fragment: residues 73-226. Synonym: mbp-a, mannan-binding protein. Engineered: yes. Mutation: yes

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116. Organ: liver. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biological unit:

Trimer (from PQS)

UniProt:

Chains A, B, C: P19999 (MBL1_RAT)

Seq:

238 a.a.

Struc:

154 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

* PDB and UniProt seqs differ at 13 residue positions (black crosses)

Resolution:

1.95Å

R-factor:

0.237

R-free:

0.269

Authors:

H.Feinberg,D.Torgerson,K.Drickamer,W.I.Weis

Key ref:

H.Feinberg et al. (2000). Mechanism of pH-dependent N-acetylgalactosamine binding by a functional mimic of the hepatocyte asialoglycoprotein receptor.. J Biol Chem, 275, 35176-35184. [PubMed id: 10931846] [DOI: 10.1074/jbc.M005557200]

Date:

03-Aug-00

Release date:

23-Aug-00

Related entries:

1fif
1fif is n-acetylgalactosamine binding mutant of mannose-
binding protein a, native.

Quick_links

Procheck

Surface

Key reference

DOI no: 10.1074/jbc.M005557200

J Biol Chem 275:35176-35184 (2000)

PubMed id: 10931846

Mechanism of pH-dependent N-acetylgalactosamine binding by a functional mimic of the hepatocyte asialoglycoprotein receptor.

H.Feinberg, D.Torgersen, K.Drickamer, W.I.Weis.

ABSTRACT

Efficient release of ligands from the Ca(2+)-dependent carbohydrate-recognition domain (CRD) of the hepatic asialoglycoprotein receptor at endosomal pH requires a small set of conserved amino acids that includes a critical histidine residue. When these residues are incorporated at corresponding positions in an homologous galactose-binding derivative of serum mannose-binding protein, the pH dependence of ligand binding becomes more like that of the receptor. The modified CRD displays 40-fold preferential binding to N-acetylgalactosamine compared with galactose, making it a good functional mimic of the asialoglycoprotein receptor. In the crystal structure of the modified CRD bound to N-acetylgalactosamine, the histidine (His(202)) contacts the 2-acetamido methyl group and also participates in a network of interactions involving Asp(212), Arg(216), and Tyr(218) that positions a water molecule in a hydrogen bond with the sugar amide group. These interactions appear to produce the preference for N-acetylgalactosamine over galactose and are also likely to influence the pK(a) of His(202). Protonation of His(202) would disrupt its interaction with an asparagine that serves as a ligand for Ca(2+) and sugar. The structure of the modified CRD without sugar displays several different conformations that may represent structures of intermediates in the release of Ca(2+) and sugar ligands caused by protonation of His(202).

Selected figure(s)

Figure 2.
Fig. 2. Coordination in the principal Ca^2+ site of QPDWG-HDRPY. Carbon, nitrogen, oxygen, and calcium are represented as white, blue, red, and green spheres, respectively. Hydrogen bonds are shown as dashed black lines, and Ca^2+ coordination bonds are solid green lines. a, GalNAc complex, copy A. b, native, copy A. c, native, copy C. The two alternate conformations of Asn210 are shown. d, native, copy B. e, stereo view of superimposed copy A of the GalNAc complex (white bonds) and native copy B (yellow bonds). f, schematic drawing of the 8-coordinate Ca^2+ site in native copy A. g, schematic drawing of the rearranged, 7-coordinate Ca^2+ site in native copy B. The diagrams in f and g are in approximately the same orientation shown in b and d, respectively, and emphasize the rotation of the pentagonal equatorial coordination plane.

Figure 4.
Fig. 4. Conformational differences around the principal Ca^2+ site. The color scheme is the same as in Fig. 1a. Ca^2+ 1 and 2 are the auxiliary and principal sites, respectively. a, native QPDWG-HDRPY, copy A. b, native QPDWG-HDRPY, copy B. c, copy B of apo-MBP-C (23). d, superposition of QPDWG-HDRPY copy A (blue), QPDWG-HDRPY copy B (red), and apo-MBP-C copy B (green).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2000, 275, 35176-35184) copyright 2000.

Figures were selected by an automated process.