Allostery: Haemoglobin (part 2)- Structure

Index to Course Material Index to Section 12 Part 1; Part 3

The subunits of haemoglobin

The alpha and beta subunits are homologous. They have the standard globin fold, but the alpha chains have one fewer helix than the beta chains or myoglobin : the D helix is replaced by a loop region. Here is a diagram of the haemoglobin fold (32Kb). (Compare this to the myoglobin fold 32Kb.)

Examine these structures:

one alpha and one beta subunit of oxyhaemoglobin; a symmetry operation must be applied to this structure to obtain the complete tetramer (more about this later on this page) 1hho (210Kb) [Bbk|BNL|ExP|Waw|Hal] Use the RasMol command restrict *a and protein in order to view only a single monomer (alpha chain). Then render this as ribbons, and colour the molecule by 'group'. Then keep this window open, for more scripts below.
myoglobin 1mba (114Kb) [Bbk|BNL|ExP|Waw|Hal].

The Haem Prosthetic Group

Haem (Fe-protoporphyrin IX) consists of a porphyrin ring with an iron atom bound to the four nitrogens at the centre.

Click here for a diagram of haem. Apply this SCRIPT to the 1hho haemoglobin structure (see above).

The haem group is situated between helices E and F, and is surrounded by non-polar residues except for the its carboxylate groups exposed at the protein surface (here is a diagram, 82Kb), and for two of the protein's histidine side chains (here is a SCRIPT for the 1hho structure, which highlights the haem and colours these histidines blue). One of these (His 87 in alpha subunit, His 92 in beta), part of helix F, binds directly to the iron atom of the haem group (the NE2 atom of the His side chain occupies one of the six coordination positions of the iron). This His is in each subunit called the proximal histidine. The distal histidine occurs in helix E (His 58 in alpha subunit, His 63 in beta). This is near to the opposite coordination position, but does not occupy it; this coordination site is occupied by oxygen in oxyhaemoglobin.

Here are orthogonal views of (oxy)haemoglobin illustrating the positions of the proximal and distal histidines in relation to the haem. SCRIPT for 1hho

The above script labels each of the helices. Note that the alpha subunit has only 7 helices (helix D is missing, or described as 'degenerate' consisting of only 2 residues), but they are named as in the scheme for the typical 8-helix globin fold.

Is helix D present in the beta subunit? Of how many residues does it consist? Refer to the heading of the pdb file.

Quaternary structure

The orientation of the four subunits in the tetrameric haemoglobin molecule is indicated in this diagram.

The crystal structure of deoxyhaemoglobin is a complete tetramer (2 alpha and 2 beta subunits) 2hhb (419Kb) [Bbk|BNL|ExP|Waw|Hal] This SCRIPT provides a similar rendition to the above diagram. Keep the RasMol window open with the 2hhb structure.

Swiss-3D prot provide this diagram.

What type of symmetry does the tetramer have? For further information refer to the symmetry page of the previous section (on Quaternary Structure).

Deoxyhaemoglobin: the T state

A number of salt bridges occur in the Tense state which are broken in the Relaxed state:

The carboxyl terminus group (residue Arg 141) of each alpha subunit makes a salt bridge with the amino terminus group (residue Val 1) of the other alpha subunit
The side chain of the Arg 141 C-terminal residue of each alpha subunit interacts with the Asp 126 side chain of the other alpha subunit
Lys 40 of each alpha subunit salt bridges with the C-terminus group (residue His 146) of the beta subunit of the other "dimer"; i.e. Lys 40 of alpha 1 interacts with C-terminus of beta 2.
The side chain of the His 146 C-terminal residue of each beta subunit interacts with Asp 94 of the same chain.

This diagram illustrates (1) and (2) of the above.

SCRIPT

This diagram illustrates (3) and (4). SCRIPT

This SCRIPT displays only the backbone atoms, except for the residues involved in the interactions above, whose side chains are displayed. They are also labelled; to turn these off type:

select
label off

The haem group of deoxyhaemoglobin is domed rather than planar. This relates to the ionic radius of the iron, which is in a high-spin Fe(II) state. The iron is too large (radius 2.06Å) to fit in the ring of nitrogens with which it coordinates; it is 0.6Å out of the plane of the ring, which is therefore distorted.

Close-up
and a perpendicular view

SCRIPT To obtain the perpendicular view, type:

rotate y -90
zoom 450
slab

Oxyhaemoglobin: the R state

The salt bridges listed for the T state in the previous section are broken in the R state. The carboxyl-terminal residues of all the subunits are able to rotate.

In contrast to deoxyhaemoglobin, the haem group is planar and the iron ion lies in the plane of the ring, as it is in a low-spin Fe(II) state with a smaller radius (1.98Å). All six coordination positions of the ion are occupied: the bound oxygen molecule accounts for the sixth.

Close-up

Perpendicular view:

Close-up

This rendition is obtained by applying the SCRIPT used earlier in this page to the 1hho oxyhaemoglobin structure (or the tetrameric form of 1hho; see below). The link to the 1hho crystal structure is at the top of this page.

Recall that the 1hho oxyhaemoglobin crystal structure contains only one alpha and one beta subunit (because the other half of the tetramer is related by crystal symmetry). You can also download the complete oxyhaemoglobin tetramer (333Kb) (provided by Brookhaven).

Index to Course Material

Index to Section 12

Part 1;

Part 3

Last updated 8th Jul '96