PDBsum entry: 1po5

Oxidoreductase

PDB id: 1po5

Contents

Protein chain

465 a.a. *

Ligands

HEM

Waters ×261

* Residue conservation analysis

PDB id:

1po5

Name:

Oxidoreductase

Title:

Structure of mammalian cytochrome p450 2b4

Structure:

Cytochrome p450 2b4. Chain: a. Synonym: cypiib4, p450-lm2, isozyme 2, p450 type b0. Engineered: yes. Mutation: yes

Source:

Oryctolagus cuniculus. Rabbit. Organism_taxid: 9986. Gene: 2b4. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

1.60Å R-factor: 0.217 R-free: 0.289

Authors:

E.E.Scott,Y.A.He,M.R.Wester,M.A.White,C.C.Chin,J.R.Halpert, E.F.Johnson,C.D.Stout

Key ref:

E.E.Scott et al. (2003). An open conformation of mammalian cytochrome P450 2B4 at 1.6-A resolution. Proc Natl Acad Sci U S A, 100, 13196-13201. PubMed id: 14563924 DOI: 10.1073/pnas.2133986100

Date:

13-Jun-03 Release date: 07-Oct-03

Protein chain

P00178  (CP2B4_RABIT) -  Cytochrome P450 2B4

Seq: 491 a.a.

Struc: 465 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.1.14.14.1 - Unspecific monooxygenase.
• Reaction: RH + reduced flavoprotein + O₂ = ROH + oxidized flavoprotein + H₂O
• Cofactor: Heme-thiolate

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

 Gene Ontology (GO) functional annotation 

• Cellular component: membrane (4 terms)
• Biological process: oxidation-reduction process (1 term)
• Biochemical function: electron carrier activity (9 terms)

Added reference

DOI no: 10.1073/pnas.2133986100

Proc Natl Acad Sci U S A 100:13196-13201 (2003)

PubMed id: 14563924

An open conformation of mammalian cytochrome P450 2B4 at 1.6-A resolution.

E.E.Scott, Y.A.He, M.R.Wester, M.A.White, C.C.Chin, J.R.Halpert, E.F.Johnson, C.D.Stout.

ABSTRACT

The xenobiotic metabolizing cytochromes P450 (P450s) are among the most versatile biological catalysts known, but knowledge of the structural basis for their broad substrate specificity has been limited. P450 2B4 has been frequently used as an experimental model for biochemical and biophysical studies of these membrane proteins. A 1.6-A crystal structure of P450 2B4 reveals a large open cleft that extends from the protein surface directly to the heme iron between the alpha-helical and beta-sheet domains without perturbing the overall P450 fold. This cleft is primarily formed by helices B' to C and F to G. The conformation of these regions is dramatically different from that of the other structurally defined mammalian P450, 2C5/3LVdH, in which the F to G and B' to C regions encapsulate one side of the active site to produce a closed form of the enzyme. The open conformation of 2B4 is trapped by reversible formation of a homodimer in which the residues between helices F and G of one molecule partially fill the open cleft of a symmetry-related molecule, and an intermolecular coordinate bond occurs between H226 and the heme iron. This dimer is observed both in solution and in the crystal. Differences between the structures of 2C5 and 2B4 suggest that defined regions of xenobiotic metabolizing P450s may adopt a substantial range of energetically accessible conformations without perturbing the overall fold. This conformational flexibility is likely to facilitate substrate access, metabolic versatility, and product egress.

Selected figure(s)

Figure 1.
Fig. 1. The 2B4 structure and comparison with 2C5. (A) P450 2B4 is oriented to view the large cleft from the protein surface to the heme. The sequence can be traced starting at the blue N terminus and ending at the red C terminus. (B and C) Comparison of 2B4 (B) and 2C5/3LV (1N6B [PDB] ) (C) structures. Residues with the highest rms deviations between the two structures include 2B4 residues 37-50 (helix A' and adjacent residues, magenta), residues 92-140 (helix B C terminus to helix D N terminus, blue), residues 206-250 (C-terminal turn of helix F through helix G, purple), residues 275-300 (loop between helices H and I encompassing a three-residue insertion in 2B4 relative to 2C5 and N-terminal half of helix I, orange), and 474-479 ( turn between L' and [3-2], gray). Excluding these residues, the rms deviation of 324 C^ atoms between 2B4 and 2C5 is 1.08 Å. The heme group is shown as a stick figure, and the iron is shown as a red sphere. N and C termini are labeled. Unless otherwise noted, molecular figures were generated by using PYMOL (28).

Figure 2.
Fig. 2. Comparison of structural elements composing the 2B4 cleft. (A) Clefts in the mammalian 2B4 (green) and the bacterial 154C1 (PDB ID code 1GWI [PDB] , blue) P450s are composed of similar structural elements. (B) In 2B4 (green) helices, F' and G' flex away from the B' helix, whereas in 2C5 (yellow), they extend to form the roof of the active site. For clarity, only the regions including helices B through D, F through G, and I are shown. The heme is shown as a stick figure.

Figures were selected by an automated process.