PDBsum entry 1e83

Electron transport

PDB id: 1e83

Contents

Protein chain

126 a.a. *

Ligands

HEC

Waters ×153

* Residue conservation analysis

PDB id:

1e83

Name:

Electron transport

Title:

Cytochrome c' from alcaligenes xylosoxidans - oxidized structure

Structure:

Cytochrome c'. Chain: a

Source:

Alcaligenes xylosoxidans. Organism_taxid: 85698. Strain: ncib 11015. Cellular_location: periplasm. Other_details: formerly known as alcaligenes sp.

Biol. unit:

Homo-Dimer (from PDB file)

Resolution:

2.05Å R-factor: 0.192 R-free: 0.252

Authors:

D.M.Lawson,C.E.M.Stevenson,C.R.Andrew,R.R.Eady

Key ref:

D.M.Lawson et al. (2000). Unprecedented proximal binding of nitric oxide to heme: implications for guanylate cyclase. EMBO J, 19, 5661-5671. PubMed id: 11060017 DOI: 10.1093/emboj/19.21.5661

Date:

15-Sep-00 Release date: 06-Nov-00

Protein chain

P00138  (CYCP_ALCXX) -  Cytochrome c' from Alcaligenes xylosoxydans xylosoxydans

Seq: 127 a.a.

Struc: 126 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1093/emboj/19.21.5661

EMBO J 19:5661-5671 (2000)

PubMed id: 11060017

Unprecedented proximal binding of nitric oxide to heme: implications for guanylate cyclase.

D.M.Lawson, C.E.Stevenson, C.R.Andrew, R.R.Eady.

ABSTRACT

Microbial cytochromes c' contain a 5-coordinate His-ligated heme that forms stable adducts with nitric oxide (NO) and carbon monoxide (CO), but not with dioxygen. We report the 1.95 and 1.35 A resolution crystal structures of the CO- and NO-bound forms of the reduced protein from Alcaligenes xylosoxidans. NO disrupts the His-Fe bond and binds in a novel mode to the proximal face of the heme, giving a 5-coordinate species. In contrast, CO binds 6-coordinate on the distal side. A second CO molecule, not bound to the heme, is located in the proximal pocket. Since the unusual spectroscopic properties of cytochromes c' are shared by soluble guanylate cyclase (sGC), our findings have potential implications for the activation of sGC induced by the binding of NO or CO to the heme domain.

Selected figure(s)

Figure 1.
Figure 1 Ribbon representation of a single subunit of the reduced Axcyt c' structure showing the position of the heme. Also depicted are the side chains of the proximal His, Leu16 and the two Cys residues that form thioether bridges to the heme. The Leu blocks access to the vacant sixth coordination site in the distal pocket. The location of the crystallographic 2-fold axis is indicated, which is perpendicular to the plane of the paper. A 180° rotation of this subunit about the 2-fold axis generates the second subunit of the functional dimer. The structure is colored with respect to sequence number, starting with blue at the N-terminus and finishing with red at the C-terminus. This figure was produced using MOLSCRIPT (Kraulis, 1991) and Raster3D (Merritt and Bacon, 1997).

Figure 3.
Figure 3 Omit difference maps for the (A) NO- and (B) CO-bound Axcyt c' structures contoured at 3.5 . All the displayed atoms were omitted from the refinements (see Materials and methods). However, Arg124 was retained in the refinement, in order to remove distracting density, in particular from the NO ligand. The view is chosen to emphasize the flattening of the heme plane upon binding of CO. The atoms are colored according to their temperature factors, which all lie roughly in the range 10–40 Å^2, where dark blue indicates a low value increasing through light blue, dark green, light green, yellow and orange, to red, which indicates a high value. Note that the side chain of His120 in the NO-bound structure and the side chain of Leu16 and the propionate group A in the CO-bound structure are less well defined in the electron density and have relatively high thermal parameters. See main text for a further explanation.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2000, 19, 5661-5671) copyright 2000.

Figures were selected by the author.

Author's comment

Cytochrome c' (cyt c') is found in the periplasmic space of denitrifying bacteria where it is thought to mediate the transfer of nitric oxide (NO) between the nitrogen cycle enzymes dissimilatory nitrite reductase and nitric oxide reductase. It contains a 5-coordinate (5c) His-ligated heme that shares spectroscopic and ligand binding properties with the heme group in the sensory domain of soluble guanylate cyclase (sGC). The latter is an extremely important enzyme involved in the control of vasodilation and blood clotting. Curiously, the enzyme is activated up to 200-fold by the binding of NO to the heme, whereas the binding of carbon monoxide (CO) gives rise to only a mild stimulation of activity.
Through X-ray crystallography we have studied NO and CO binding to cyt c'. CO binds to the distal face to give a 6-coordinate (6c) adduct. By contrast, NO binding gives rise to a 5c adduct through the displacement of the proximal His, to give a novel and unexpected proximal binding mode for NO. These results are also supported by a range of spectroscopies. We propose that cyt c' provides a structural model for the heme domain of this enzyme and thereby helps to explain the differential effects of NO and CO on its activity.
David Lawson