PDBsum entry 1b5a

Electron transport

PDB id: 1b5a

Contents

Protein chain

94 a.a. *

Ligands

HEM

* Residue conservation analysis

PDB id:

1b5a

Name:

Electron transport

Title:

Rat ferrocytochrome b5 a conformation, nmr, 1 structure

Structure:

Ferrocytochrome b5. Chain: a. Engineered: yes. Other_details: heme as prosthetic group, with h63 and h39 as axial ligands

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

NMR struc:

1 models

Authors:

B.Dangi,S.Sarma,C.Yan,D.Banville,R.D.Guiles

Key ref:

B.Dangi et al. (1998). The origin of differences in the physical properties of the equilibrium forms of cytochrome b5 revealed through high-resolution NMR structures and backbone dynamic analyses. Biochemistry, 37, 8289-8302. PubMed id: 9622481 DOI: 10.1021/bi9801964

Date:

06-Apr-98 Release date: 17-Jun-98

Protein chain

P00173  (CYB5_RAT) -  Cytochrome b5 from Rattus norvegicus

Seq: 134 a.a.

Struc: 94 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1021/bi9801964

Biochemistry 37:8289-8302 (1998)

PubMed id: 9622481

The origin of differences in the physical properties of the equilibrium forms of cytochrome b5 revealed through high-resolution NMR structures and backbone dynamic analyses.

B.Dangi, S.Sarma, C.Yan, D.L.Banville, R.D.Guiles.

ABSTRACT

On the basis of a comparison of high-resolution solution structures calculated for both equilibrium forms of rat ferrocytochrome b5, differences in reduction potential and thermodyanmic stability have been characterized in terms of significant structural and dynamic differences between the two forms. The dominant difference between A and B conformations has long been known to be due to a 180 degrees rotation of the heme in the binding pocket about an axis defined by the alpha- and gamma-meso carbons, however, the B form has not been structurally characterized until now. The most significant differences observed between the two forms were the presence of a hydrogen bond between the 7-propionate and the S64 amide in the A form but not the B form and surprisingly a displacement of the heme out of the binding pocket by 0.9 A in the B form relative to the A form. The magnitude of other factors which could contribute to the known difference in reduction potentials in the bovine protein [Walker, F. A., Emrick, D., Rivera, J. E., Hanquet, B. J., and Buttlaire, D. H. (1988) J. Am. Chem. Soc. 110, 6234-6240], such as differences in the orientation of the axial imidazoles and differences in hydrogen bond strength to the imidazoles, have been evaluated. The dominant effector of the reduction potential would appear to be the lack of the hydrogen bond to the S64 amide in the B form which frees up the propionate to charge stabilize the iron in the oxidized state and thus lower the reduction potential of the B form. The structure we report for the A form, based on heteronuclear NMR restraints, involving a total of 1288 restraints strongly resembles both the X-ray crystal structure of the bovine protein and a recently reported structure for the A form of the rat protein based on homonuclear data alone [Banci, L., Bertini, I., Ferroni, F., and Rosato, A. (1997) Eur. J. Biochem. 249, 270-279]. The rmsd for the backbone atoms of the A form is 0.54 A (0.92 A for all non-hydrogens). The rmsd for the backbone of the B form is 0.51 A (0. 90 A for all non-hydrogen atoms). An analysis of backbone dynamics based on a model-free analysis of 15N relaxation data, which incorporated axially symmetric diffusion tensor modeling of the cytochrome, indicates that the protein is more rigid in the reduced state relative to the oxidized state, based on a comparison with order parameters reported for the bovine protein in the oxidized state [Kelly, G. P., Muskett, F. W., and Whitford, D. (1997) Eur. J. Biochem. 245, 349-354].