2D2N

Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi

Summary for 2D2N

• Entry DOI: 10.2210/pdb2d2n/pdb
• Related: 2D2M
• Descriptor: Giant hemoglobin, A1(b) globin chain, Giant hemoglobin, A2(a5) globin chain, Giant hemoglobin, B2(c) globin chain, ... (7 entities in total)
• Functional Keywords: giant hemoglobin, sulfide binding, invertebrate, pogonophora, oligobrachia mashikoi, oxygen storage-transport complex, oxygen storage/transport
• Biological source: Oligobrachia mashikoi; More
• Cellular location: Secreted: Q7M419 Q7M413 Q7M418 Q5KSB7
• Total number of polymer chains: 4
• Total formula weight: 64380.10

Authors

Numoto, N.,Nakagawa, T.,Kita, A.,Sasayama, Y.,Fukumori, Y.,Miki, K. (deposition date: 2005-09-12, release date: 2005-10-25, Last modification date: 2024-10-23)

Primary citation

Numoto, N.,Nakagawa, T.,Kita, A.,Sasayama, Y.,Fukumori, Y.,Miki, K.
Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi.
Proc.Natl.Acad.Sci.USA, 102:14521-14526, 2005

PubMed Abstract: Mouthless and gutless marine animals, pogonophorans and vestimentiferans, obtain their nutrition solely from their symbiotic chemoautotrophic sulfur-oxidizing bacteria. These animals have sulfide-binding 400-kDa and/or 3,500-kDa Hb, which transports oxygen and sulfide simultaneously. The symbiotic bacteria are supplied with sulfide by Hb of the host animal and use it to provide carbon compounds. Here, we report the crystal structure of a 400-kDa Hb from pogonophoran Oligobrachia mashikoi at 2.85-A resolution. The structure is hollow-spherical, composed of a total of 24 globins as a dimer of dodecamer. This dodecameric assemblage would be a fundamental structural unit of both 400-kDa and 3,500-kDa Hbs. The structure of the mercury derivative used for phasing provides insights into the sulfide-binding mechanism. The mercury compounds bound to all free Cys residues that have been expected as sulfide-binding sites. Some of the free Cys residues are surrounded by Phe aromatic rings, and mercury atoms come into contact with these residues in the derivative structure. It is strongly suggested that sulfur atoms bound to these sites could be stabilized by aromatic-electrostatic interactions by the surrounding Phe residues.

PubMed: 16204001
DOI: 10.1073/pnas.0501541102

Experimental method

X-RAY DIFFRACTION (3.2 Å)