PDBsum entry 2zs1

Oxygen storage, oxygen transport

PDB id: 2zs1

Contents

Protein chains

140 a.a. *

142 a.a. *

147 a.a. *

155 a.a. *

Ligands

HEM-OXY ×4

GOL ×6

Metals

_CL

_MG

Waters ×643

* Residue conservation analysis

PDB id:

2zs1

Name:

Oxygen storage, oxygen transport

Title:

Structural basis for the heterotropic and homotropic interactions of invertebrate giant hemoglobin

Structure:

Extracellular giant hemoglobin major globin subunit a1. Chain: a. Synonym: major globin chain b. Extracellular giant hemoglobin major globin subunit a2. Chain: b. Synonym: major globin chain a5. Extracellular giant hemoglobin major globin subunit b2. Chain: c. Synonym: major globin chain c.

Source:

Oligobrachia mashikoi. Beard worm. Organism_taxid: 55676. Organism_taxid: 55676

Resolution:

1.70Å R-factor: 0.180 R-free: 0.207

Authors:

N.Numoto,T.Nakagawa,A.Kita,Y.Sasayama,Y.Fukumori,K.Miki

Key ref:

N.Numoto et al. (2008). Structural basis for the heterotropic and homotropic interactions of invertebrate giant hemoglobin. Biochemistry, 47, 11231-11238. PubMed id: 18834142

Date:

02-Sep-08 Release date: 21-Oct-08

Protein chain

Q7M419  (GLBA1_OLIMA) -  Extracellular giant hemoglobin major globin subunit A1 from Oligobrachia mashikoi

Seq: 156 a.a.

Struc: 140 a.a.

Protein chain

Q7M413  (GLBA2_OLIMA) -  Extracellular giant hemoglobin major globin subunit A2 from Oligobrachia mashikoi

Seq: 158 a.a.

Struc: 142 a.a.

Protein chain

Q7M418  (GLBB2_OLIMA) -  Extracellular giant hemoglobin major globin subunit B2 from Oligobrachia mashikoi

Seq: 163 a.a.

Struc: 147 a.a.

Protein chain

Q5KSB7  (GLBB1_OLIMA) -  Extracellular giant hemoglobin major globin subunit B1 from Oligobrachia mashikoi

Seq: 161 a.a.

Struc: 155 a.a.*

* PDB and UniProt seqs differ at 11 residue positions (black crosses)

Biochemistry 47:11231-11238 (2008)

PubMed id: 18834142

Structural basis for the heterotropic and homotropic interactions of invertebrate giant hemoglobin.

N.Numoto, T.Nakagawa, A.Kita, Y.Sasayama, Y.Fukumori, K.Miki.

ABSTRACT

The oxygen binding properties of extracellular giant hemoglobins (Hbs) in some annelids exhibit features significantly different from those of vertebrate tetrameric Hbs. Annelid giant Hbs show cooperative oxygen binding properties in the presence of inorganic cations, while the cooperativities of vertebrate Hbs are enhanced by small organic anions or chloride ions. To elucidate the structural basis for the cation-mediated cooperative mechanisms of these giant Hbs, we determined the crystal structures of Ca2+- and Mg2+-bound Hbs from Oligobrachia mashikoi at 1.6 and 1.7 A resolution, respectively. Both of the metal-bound structures were determined in the oxygenated state. Four Ca2+-binding sites and one Mg2+-binding site were identified in each tetramer subassembly. These cations are considered to stabilize the oxygenated form and increase affinity and cooperativity for oxygen binding, as almost all of the Ca2+ and Mg2+ cations were bound at the interface regions, forming either direct or hydrogen bond-mediated interactions with the neighboring subunits. A comparison of the structures of the oxygenated form and the partially unliganded form provides structural insight into proton-coupled cooperativity (Bohr effect) and ligand-induced transitions. Two histidine residues are assumed to be primarily associated with the Bohr effect. With regard to the ligand-induced cooperativity, a novel quaternary rotation mechanism is proposed to exist at the interface region of the dimer subassembly. Interactions among conserved residues Arg E10, His F3, Gln F7, and Val E11, together with the bending motion of the heme molecules, appear to be essential for quaternary rearrangement.