PDBsum entry 2bb5

Transport protein

PDB id: 2bb5

Contents

Protein chain

409 a.a. *

Ligands

B12 ×2

Waters ×8

* Residue conservation analysis

PDB id:

2bb5

Name:

Transport protein

Title:

Structure of human transcobalamin in complex with cobalamin

Structure:

Transcobalamin ii. Chain: a, b. Synonym: tcii, tc ii. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: tcn2, tc2. Expressed in: pichia pastoris. Expression_system_taxid: 4922.

Resolution:

3.20Å R-factor: 0.258 R-free: 0.288

Authors:

J.Wuerges,G.Garau,S.Geremia,S.N.Fedosov,T.E.Petersen,L.Randaccio

Key ref:

J.Wuerges et al. (2006). Structural basis for mammalian vitamin B12 transport by transcobalamin. Proc Natl Acad Sci U S A, 103, 4386-4391. PubMed id: 16537422 DOI: 10.1073/pnas.0509099103

Date:

17-Oct-05 Release date: 04-Apr-06

Protein chains

P20062  (TCO2_HUMAN) -  Transcobalamin-2 from Homo sapiens

Seq: 427 a.a.

Struc: 409 a.a.*

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

DOI no: 10.1073/pnas.0509099103

Proc Natl Acad Sci U S A 103:4386-4391 (2006)

PubMed id: 16537422

Structural basis for mammalian vitamin B12 transport by transcobalamin.

J.Wuerges, G.Garau, S.Geremia, S.N.Fedosov, T.E.Petersen, L.Randaccio.

ABSTRACT

Cobalamin (Cbl, vitamin B(12)) serves for two essential cofactors in mammals. The pathway for its intestinal absorption, plasma transport, and cellular uptake uses cell surface receptors and three Cbl-transporting proteins, haptocorrin, intrinsic factor, and transcobalamin (TC). We present the structure determination of a member of the mammalian Cbl-transporter family. The crystal structures of recombinant human and bovine holo-TCs reveal a two-domain architecture, with an N-terminal alpha(6)-alpha(6) barrel and a smaller C-terminal domain. One Cbl molecule in base-on conformation is buried inside the domain interface. Structural data combined with previous binding assays indicate a domain motion in the first step of Cbl binding. In a second step, the weakly coordinated ligand H(2)O at the upper axial side of added H(2)O-Cbl is displaced by a histidine residue of the alpha(6)-alpha(6) barrel. Analysis of amino acid conservation on TC's surface in orthologous proteins suggests the location of the TC-receptor-recognition site in an extended region on the alpha(6)-alpha(6) barrel. The TC structure allows for the mapping of sites of amino acid variation due to polymorphisms of the human TC gene. Structural information is used to predict the overall fold of haptocorrin and intrinsic factor and permits a rational approach to the design of new Cbl-based bioconjugates for diagnostic or therapeutic drug delivery.

Selected figure(s)

Figure 2.
Fig. 2. Cbl interactions with bovine TC (monoclinic crystal form). (A) Stereoview of the F[o] - F[c] omit electron density map at 2.0-Å resolution around the coordination of His-175 N to the Co ion of Cbl (contour level 3 ). Some solvent water molecules are shown as red spheres, one of which forms a H-bond to His-175 N . The Co ion (magenta) is axially coordinated by the imidazole N at a distance of 2.13 Å (above the corrin plane) and by the dimethylbenzimidazole nitrogen N3B at 2.09 Å. (B) Scheme of polar interactions. H-bonds are shown as dotted lines (red, to residues in the -domain; blue, to residues in the -domain; green, solvent-mediated interactions). The main or side chain is indicated for residues in direct contact with Cbl, whereas dots indicate residues linked to Cbl via solvent molecules (11 H[2]O and a Cl- ion from NaCl salt). The same scheme of direct contacts is observed in human TC (to translate from bovine to human TC numbering, see Fig. 3).

Figure 5.
Fig. 5. Mapping the amino acid conservation among seven TCs (Fig. 9B) on the molecular surface of human TC. Color coding: red, identity; orange, conserved; yellow, semiconserved; white, not conserved. The view to the -domain is as in Fig. 1C. The conserved region proposed as TC's receptor-recognition site is located on the right half and involves the surface of the labeled helices 3- 6 and their loops. A low level of conservation is present on the -domain surface.

Figures were selected by the author.