1V5H

Crystal Structure of Human Cytoglobin (Ferric Form)

Summary for 1V5H

• Entry DOI: 10.2210/pdb1v5h/pdb
• Descriptor: Cytoglobin, PROTOPORPHYRIN IX CONTAINING FE (3 entities in total)
• Functional Keywords: globin, heme, oxygen transport, oxygen storage, ligand binding, riken structural genomics/proteomics initiative, rsgi, structural genomics, oxygen storage-transport complex, oxygen storage/transport
• Biological source: Homo sapiens (human)
• Cellular location: Cytoplasm (By similarity): Q8WWM9
• Total number of polymer chains: 1
• Total formula weight: 22332.38

Authors

Sugimoto, H.,Makino, M.,Sawai, H.,Kawada, N.,Yoshizato, K.,Shiro, Y.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2003-11-23, release date: 2004-06-08, Last modification date: 2023-12-27)

Primary citation

Sugimoto, H.,Makino, M.,Sawai, H.,Kawada, N.,Yoshizato, K.,Shiro, Y.
Structural basis of human cytoglobin for ligand binding.
J.Mol.Biol., 339:873-885, 2004

PubMed Abstract: Cytoglobin (Cgb), a newly discovered member of the vertebrate globin family, binds O(2) reversibly via its heme, as is the case for other mammalian globins (hemoglobin (Hb), myoglobin (Mb) and neuroglobin (Ngb)). While Cgb is expressed in various tissues, its physiological role is not clearly understood. Here, the X-ray crystal structure of wild type human Cgb in the ferric state at 2.4A resolution is reported. In the crystal structure, ferric Cgb is dimerized through two intermolecular disulfide bonds between Cys38(B2) and Cys83(E9), and the dimerization interface is similar to that of lamprey Hb and Ngb. The overall backbone structure of the Cgb monomer exhibits a traditional globin fold with a three-over-three alpha-helical sandwich, in which the arrangement of helices is basically the same among all globins studied to date. A detailed comparison reveals that the backbone structure of the CD corner to D helix region, the N terminus of the E-helix and the F-helix of Cgb resembles more closely those of pentacoordinated globins (Mb, lamprey Hb), rather than hexacoordinated globins (Ngb, rice Hb). However, the His81(E7) imidazole group coordinates directly to the heme iron as a sixth axial ligand to form a hexcoordinated heme, like Ngb and rice Hb. The position and orientation of the highly conserved residues in the heme pocket (Phe(CD1), Val(E11), distal His(E7) and proximal His(F8)) are similar to those of other globin proteins. Two alternative conformations of the Arg84(E10) guanidium group were observed, suggesting that it participates in ligand binding to Cgb, as is the case for Arg(E10) of Aplysia Mb and Lys(E10) of Ngb. The structural diversities and similarities among globin proteins are discussed with relevance to molecular evolutionary relationships.

PubMed: 15165856
DOI: 10.1016/j.jmb.2004.04.024

Experimental method

X-RAY DIFFRACTION (2.4 Å)