3AG0

Crystal structure of carbonmonoxy human cytoglobin

Summary for 3AG0

• Entry DOI: 10.2210/pdb3ag0/pdb
• Related: 1v5h 2DC3
• Descriptor: Cytoglobin, PROTOPORPHYRIN IX CONTAINING FE, CARBON MONOXIDE, ... (4 entities in total)
• Functional Keywords: globins, heme, carbon monoxide, complex, ligands, hexacoordination, bis-his, disulfide bond, iron, metal-binding, oxygen transport, transport
• Biological source: Homo sapiens (human)
• Cellular location: Cytoplasm (By similarity): Q8WWM9
• Total number of polymer chains: 1
• Total formula weight: 22222.24

Authors

Makino, M.,Sawai, H.,Shiro, Y.,Sugimoto, H. (deposition date: 2010-03-17, release date: 2011-02-02, Last modification date: 2023-11-08)

Primary citation

Makino, M.,Sawai, H.,Shiro, Y.,Sugimoto, H.
Crystal structure of the carbon monoxide complex of human cytoglobin
Proteins, 79:1143-1153, 2011

PubMed Abstract: Cytoglobin (Cgb) is a vertebrate heme-containing globin-protein expressed in a broad range of mammalian tissues. Unlike myoglobin, Cgb displays a hexa-coordinated (bis-hystidyl) heme iron atom, having the heme distal His81(E7) residue as the endogenous sixth ligand. In the present study, we crystallized human Cgb in the presence of a reductant Na₂S₂O₄ under a carbon monoxide (CO) atmosphere, and determined the crystal structure at 2.6 A resolution. The CO ligand occupies the sixth axial position of the heme ferrous iron. Eventually, the imidazole group of His81(E7) is expelled from the sixth position and swings out of the distal heme pocket. The flipping motion of the His81 imidazole group accompanies structural readjustments of some residues (Gln62, Phe63, Gln72, and Ser75) in both the CD-corner and D-helix regions of Cgb. On the other hand, no significant structural changes were observed in other Cgb regions, for example, on the proximal side. These structural alterations that occurred as a result of exogenous ligand (CO) binding are clearly different from those observed in other vertebrate hexa-coordinated globins (mouse neuroglobin, Drosophila melanogaster hemoglobin) and penta-coordinated sperm whale myoglobin. The present study provides the structural basis for further discussion of the unique ligand-binding properties of Cgb.

PubMed: 21254233
DOI: 10.1002/prot.22950

Experimental method

X-RAY DIFFRACTION (2.6 Å)