PDBsum entry 1v5h

Oxygen storage/transport

PDB id: 1v5h

Contents

Protein chain

151 a.a. *

Ligands

HEM

Waters ×30

* Residue conservation analysis

PDB id:

1v5h

Name:

Oxygen storage/transport

Title:

Crystal structure of human cytoglobin (ferric form)

Structure:

Cytoglobin. Chain: a. Synonym: histoglobin, hgb, stellate cell activation-associated protein. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: cygb, stap. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.40Å R-factor: 0.248 R-free: 0.250

Authors:

H.Sugimoto,M.Makino,H.Sawai,N.Kawada,K.Yoshizato,Y.Shiro,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

H.Sugimoto et al. (2004). Structural basis of human cytoglobin for ligand binding. J Mol Biol, 339, 873-885. PubMed id: 15165856 DOI: 10.1016/j.jmb.2004.04.024

Date:

23-Nov-03 Release date: 08-Jun-04

Protein chain

Q8WWM9  (CYGB_HUMAN) -  Cytoglobin from Homo sapiens

Seq: 190 a.a.

Struc: 151 a.a.

DOI no: 10.1016/j.jmb.2004.04.024

J Mol Biol 339:873-885 (2004)

PubMed id: 15165856

Structural basis of human cytoglobin for ligand binding.

H.Sugimoto, M.Makino, H.Sawai, N.Kawada, K.Yoshizato, Y.Shiro.

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.

Selected figure(s)

Figure 1.
Figure 1. Stereo diagram of the final electron density map around the heme of Cgb from (a) parallel with the heme plane and (b) distal side of heme plane. The sigmaA[57.] weighted 2mF[o] -DF[c] map is contoured at the 1.1s level. The final refined coordinates for Cgb are superimposed. Oxygen and nitrogen atoms are coloured red and blue, respectively. The distal and proximal His and heme are coloured in gold stick. Other residues are in gray stick. The imidazole groups of His81(E7) and His113(F8) bind to the heme iron as endogenous axial ligands to form the hexacoordinated structure. The iron-bound imidazole of distal His81(E7) is surrounded by Phe60(CD1) and Val85(E11), which are located on the porphyrin pyrrols D and B, respectively. Arg84(E10) in the distal side is also close the heme and exhibits alternative conformations. The Figure was prepared with program O.[51.]

Figure 7.
Figure 7. Comparison of the CD, D, E and F helices regions. The 33 atoms in the heme plane were used in the least-squares fitting. Cgb (green) is superimposed on (a) Mb (blue), (b) rice Hb (gray), (c) Ngb (orange) or (d) sea lamprey Hb (red). The distal and proximal His and heme are represented by a stick model.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 339, 873-885) copyright 2004.

Figures were selected by an automated process.