PDBsum entry 1gvh

Oxidoreductase

PDB id: 1gvh

Contents

Protein chain

396 a.a. *

Ligands

FAD

HEM

Metals

_CL

_NA ×2

Waters ×191

* Residue conservation analysis

PDB id:

1gvh

Name:

Oxidoreductase

Title:

The x-ray structure of ferric escherichia coli flavohemoglobin reveals an unespected geometry of the distal heme pocket

Structure:

Flavohemoprotein. Chain: a. Synonym: flavohemoglobin, dihydropteridine reductase, hemoglobin-like protein, dihydropteridine reductase, ferrisiderophore reductase b, nitric oxide dioxygenase, nod. Ec: 1.6.99.7

Source:

Escherichia coli. Organism_taxid: 562

Biol. unit:

Dodecamer (from PDB file)

Resolution:

2.19Å R-factor: 0.187 R-free: 0.247

Authors:

A.Ilari,K.A.Johnson,A.Bonamore,A.Farina,A.Boffi

Key ref:

A.Ilari et al. (2002). The X-ray structure of ferric Escherichia coli flavohemoglobin reveals an unexpected geometry of the distal heme pocket. J Biol Chem, 277, 23725-23732. PubMed id: 11964402 DOI: 10.1074/jbc.M202228200

Date:

13-Feb-02 Release date: 06-Aug-02

Protein chain

P24232  (HMP_ECOLI) -  Flavohemoprotein from Escherichia coli (strain K12)

Seq: 396 a.a.

Struc: 396 a.a.

Enzyme reactions

• Enzyme class: E.C.1.14.12.17 - nitric oxide dioxygenase.
• Reaction:
  1. 2 nitric oxide + NADPH + 2 O2 = 2 nitrate + NADP⁺ + H⁺
  2. 2 nitric oxide + NADH + 2 O2 = 2 nitrate + NAD⁺ + H⁺
• Cofactor: FAD; Heme

FAD (Bound ligand (Het Group name = FAD) corresponds exactly) Heme (Bound ligand (Het Group name = HEM) matches with 95.45% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1074/jbc.M202228200

J Biol Chem 277:23725-23732 (2002)

PubMed id: 11964402

The X-ray structure of ferric Escherichia coli flavohemoglobin reveals an unexpected geometry of the distal heme pocket.

A.Ilari, A.Bonamore, A.Farina, K.A.Johnson, A.Boffi.

ABSTRACT

The x-ray structure of ferric unliganded lipid-free Escherichia coli flavohemoglobin has been solved to a resolution of 2.2 A and refined to an R-factor of 19%. The overall fold is similar to that of ferrous lipid-bound Alcaligenes eutrophus flavohemoglobin with the notable exception of the E helix positioning within the globin domain and a rotation of the NAD binding module with respect to the FAD-binding domain accompanied by a substantial rearrangement of the C-terminal region. An inspection of the heme environment in E. coli flavohemoglobin reveals an unexpected architecture of the distal pocket. In fact, the distal site is occupied by the isopropyl side chain Leu-E11 that shields the heme iron from the residues in the topological positions predicted to interact with heme iron-bound ligands, namely Tyr-B10 and Gln-E7, and stabilizes a pentacoordinate ferric iron species. Ligand binding properties are consistent with the presence of a pentacoordinate species in solution as indicated by a very fast second order combination rates with imidazole and azide. Surprisingly, imidazole, cyanide, and azide binding profiles at equilibrium are not accounted for by a single site titration curve but are biphasic and strongly suggest the presence of two distinct conformers within the liganded species.

Selected figure(s)

Figure 3.
Fig. 3. Structural overlay of the globin domains of E. coli and A. eutrophus flavohemoglobin and Vitreoscilla sp. hemoglobin. The overlay among globin domains was obtained by minimizing the C- distances for each protein using the program SEQUOIA (21) and was depicted with the program MOLSCRIPT (28). The stereo diagram of the globin domain of HMP ( red ribbons, yellow heme) is overlaid with the corresponding domain of A. eutrophus flavohemoglobin (green ribbons, green heme) in A and with Vitreoscilla Hb (cyan ribbons, blue heme) in B.

Figure 4.
Fig. 4. Structural details of the heme pocket in E. coli ferric unliganded flavohemoglobin. The heme molecule is shown in stereo together with a selection of amino acid residues within the pocket at 5 Å from the macrocycle. The phenolic ring of Tyr29-B10 located at >5 Å from the heme is also shown, whereas the Phe^43-CD1 is hidden for clarity. The picture was obtained with the program MOLSCRIPT (28).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 23725-23732) copyright 2002.

Figures were selected by an automated process.