4KKJ

Crystal Structure of Haptocorrin in Complex with Cbi


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for universal corrinoid recognition by the cobalamin transport protein haptocorrin.

Furger, E.Frei, D.C.Schibli, R.Fischer, E.Prota, A.E.

(2013) J.Biol.Chem. 288: 25466-25476

  • DOI: 10.1074/jbc.M113.483271
  • Primary Citation of Related Structures:  4KKI

  • PubMed Abstract: 
  • Cobalamin (Cbl; vitamin B12) is an essential micronutrient synthesized only by bacteria. Mammals have developed a sophisticated uptake system to capture the vitamin from the diet. Cbl transport is mediated by three transport proteins: transcobalamin, ...

    Cobalamin (Cbl; vitamin B12) is an essential micronutrient synthesized only by bacteria. Mammals have developed a sophisticated uptake system to capture the vitamin from the diet. Cbl transport is mediated by three transport proteins: transcobalamin, intrinsic factor, and haptocorrin (HC). All three proteins have a similar overall structure but a different selectivity for corrinoids. Here, we present the crystal structures of human HC in complex with cyanocobalamin and cobinamide at 2.35 and 3.0 Å resolution, respectively. The structures reveal that many of the interactions with the corrin ring are conserved among the human Cbl transporters. However, the non-conserved residues Asn-120, Arg-357, and Asn-373 form distinct interactions allowing for stabilization of corrinoids other than Cbl. A central binding motif forms interactions with the e- and f-side chains of the corrin ring and is conserved in corrinoid-binding proteins of other species. In addition, the α- and β-domains of HC form several unique interdomain contacts and have a higher shape complementarity than those of intrinsic factor and transcobalamin. The stabilization of ligands by all of these interactions is reflected in higher melting temperatures of the protein-ligand complexes. Our structural analysis offers fundamental insights into the unique binding behavior of HC and completes the picture of Cbl interaction with its three transport proteins.


    Organizational Affiliation

    Center for Radiopharmaceutical Sciences, Paul Scherrer Institut, CH-5232 Villigen PSI, Zürich, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transcobalamin-1
A
467Homo sapiensGene Names: TCN1 (TC1)
Find proteins for P20061 (Homo sapiens)
Go to Gene View: TCN1
Go to UniProtKB:  P20061
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CYN
Query on CYN

Download SDF File 
Download CCD File 
A
CYANIDE ION
C N
XFXPMWWXUTWYJX-UHFFFAOYSA-N
 Ligand Interaction
CBY
Query on CBY

Download SDF File 
Download CCD File 
A
COB(II)INAMIDE
C48 H72 Co N11 O8
GFVWZOGCSKVPRA-NZMQITGIDF
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.204 
  • Space Group: P 64
Unit Cell:
Length (Å)Angle (°)
a = 150.378α = 90.00
b = 150.378β = 90.00
c = 60.275γ = 120.00
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
XDSdata reduction
RemDAqdata collection
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-17
    Type: Initial release
  • Version 1.1: 2013-10-09
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description