PDBsum entry 1v4u

Oxygen storage/transport

PDB id: 1v4u

Contents

Protein chains

144 a.a. *

142 a.a. *

Ligands

HEM-CMO ×4

Waters ×138

* Residue conservation analysis

PDB id:

1v4u

Name:

Oxygen storage/transport

Title:

Crystal structure of bluefin tuna carbonmonoxy-hemoglobin

Structure:

Hemoglobin alpha chain. Chain: a, c. Hemoglobin beta chain. Chain: b, d

Source:

Thunnus thynnus. Bluefin tuna. Organism_taxid: 8237. Tissue: red cell. Tissue: red cell

Biol. unit:

Tetramer (from PQS)

Resolution:

2.00Å R-factor: 0.207 R-free: 0.264

Authors:

T.Yokoyama,K.T.Chong,Y.Miyazaki,T.Nakatsukasa,S.Unzai,G.Miyazaki, H.Morimoto,R.H.T.Jeremy,S.Y.Park

Key ref:

T.Yokoyama et al. (2004). Novel mechanisms of pH sensitivity in tuna hemoglobin: a structural explanation of the root effect. J Biol Chem, 279, 28632-28640. PubMed id: 15117955 DOI: 10.1074/jbc.M401740200

Date:

19-Nov-03 Release date: 06-Jul-04

Protein chains

Q8AYM0  (Q8AYM0_THUTH) -  Hemoglobin alpha chain 1 from Thunnus thynnus

Seq: 144 a.a.

Struc: 143 a.a.

Protein chains

Q8AYM1  (Q8AYM1_THUTH) -  Hemoglobin beta chain from Thunnus thynnus

Seq: 147 a.a.

Struc: 142 a.a.

DOI no: 10.1074/jbc.M401740200

J Biol Chem 279:28632-28640 (2004)

PubMed id: 15117955

Novel mechanisms of pH sensitivity in tuna hemoglobin: a structural explanation of the root effect.

T.Yokoyama, K.T.Chong, G.Miyazaki, H.Morimoto, D.T.Shih, S.Unzai, J.R.Tame, S.Y.Park.

ABSTRACT

The crystal structure of hemoglobin has been known for several decades, yet various features of the molecule remain unexplained or controversial. Several animal hemoglobins have properties that cannot be readily explained in terms of their amino acid sequence and known atomic models of hemoglobin. Among these, fish hemoglobins are well known for their widely varying interactions with heterotropic effector molecules and pH sensitivity. Some fish hemoglobins are almost completely insensitive to pH (within physiological limits), whereas others show extremely low oxygen affinity under acid conditions, a phenomenon called the Root effect. X-ray crystal structures of Root effect hemoglobins have not, to date, provided convincing explanations of this effect. Sequence alignments have signally failed to pinpoint the residues involved, and site-directed mutagenesis has not yielded a human hemoglobin variant with this property. We have solved the crystal structure of tuna hemoglobin in the deoxy form at low and moderate pH and in the presence of carbon monoxide at high pH. A comparison of these models shows clear evidence for novel mechanisms of pH-dependent control of ligand affinity.

Selected figure(s)

Figure 3.
FIG. 3. Stereo overlay of the heme pocket of tuna Hb and HbA. The deoxy form (pH 7.5) (a) and the CO form (b) are shown. HbA is shown in blue, and the residue numbers of the human protein are shown in brackets. The atoms and bonds of tuna Hb are colored by atom type as follows: yellow, carbon; red, oxygen; blue, nitrogen.

Figure 7.
FIG. 7. The C-terminal histidine of the chains in the deoxy form. The position of this residue is almost identical in the structures at pH 5 and 7.5. Ser-93 hydrogen bonds to Asp-94 through its side chain hydroxyl group (shown as a red dotted line), but the imidazole group of His-146 is too far (>3.5 Å) from the Asp for a strong bonding interaction.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 28632-28640) copyright 2004.

Figures were selected by an automated process.