PDBsum entry: 2p85

Oxidoreductase

PDB id: 2p85

Contents

Protein chains

(+ 0 more) 464 a.a. *

Ligands

HEM ×6

IND-IND ×6

Waters ×597

* Residue conservation analysis

PDB id:

2p85

Name:

Oxidoreductase

Title:

Structure of human lung cytochrome p450 2a13 with indole bound in two alternate conformations

Structure:

Cytochrome p450 2a13. Chain: a, b, c, d, e, f. Fragment: catalytic domain (residues 29-494). Synonym: cypiia13. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: cyp2a13. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.35Å R-factor: 0.219 R-free: 0.277

Authors:

E.E.Scott,C.D.Stout

Key ref:

B.D.Smith et al. (2007). Structure of the human lung cytochrome P450 2A13. J Biol Chem, 282, 17306-17313. PubMed id: 17428784 DOI: 10.1074/jbc.M702361200

Date:

21-Mar-07 Release date: 10-Apr-07

Protein chains

Q16696  (CP2AD_HUMAN) -  Cytochrome P450 2A13

Seq: 494 a.a.

Struc: 464 a.a.

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 (1 term)
• Biochemical function: electron carrier activity (9 terms)

Added reference

DOI no: 10.1074/jbc.M702361200

J Biol Chem 282:17306-17313 (2007)

PubMed id: 17428784

Structure of the human lung cytochrome P450 2A13.

B.D.Smith, J.L.Sanders, P.R.Porubsky, G.H.Lushington, C.D.Stout, E.E.Scott.

ABSTRACT

The human lung cytochrome P450 2A13 (CYP2A13) activates the nicotine-derived procarcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) into DNA-altering compounds that cause lung cancer. Another cytochrome P450, CYP2A6, is also present in human lung, but at much lower levels. Although these two enzymes are 93.5% identical, CYP2A13 metabolizes NNK with much lower K(m) values than does CYP2A6. To investigate the structural differences between these two enzymes the structure of CYP2A13 was determined to 2.35A by x-ray crystallography and compared with structures of CYP2A6. As expected, the overall CYP2A13 and CYP2A6 structures are very similar with an average root mean square deviation of 0.5A for the Calpha atoms. Like CYP2A6, the CYP2A13 active site cavity is small and highly hydrophobic with a cluster of Phe residues composing the active site roof. Active site residue Asn(297) is positioned to hydrogen bond with an adventitious ligand, identified as indole. Amino acid differences between CYP2A6 and CYP2A13 at positions 117, 300, 301, and 208 relate to different orientations of the ligand plane in the two protein structures and may underlie the significant variations observed in binding and catalysis of many CYP2A ligands. In addition, docking studies suggest that residues 365 and 366 may also contribute to differences in NNK metabolism.

Selected figure(s)

Figure 4.
FIGURE 4. The CYP2A13 protein (blue ribbons and sticks), heme (red sticks), and indole A (cyan sticks) are shown overlaid with selected CYP2A6 residues (green sticks) that reorient the plane of coumarin (green sticks) in the active site. CYP2A13 indole B is not shown for clarity, but adopts a very similar plane to indole A.

Figure 5.
FIGURE 5. NNK docking into CYP2A6 and CYP2A13. Panel A, NNK docked into the CYP2A6 structure assumes a nonproductive orientation with the methylene and methyl carbons no closer than 7.0 and 5.5 Å from the heme iron, respectively. In contrast, NNK docked into the CYP2A13 structure assumes an orientation with either the methyl (panel B) or methylene (panel C) oriented for hydroxylation into the two carcinogenic metabolites observed experimentally. Black circles highlight methyl and methylene carbons hydroxylated to form carcinogenic metabolites. Residues and helices shown are as described in the legend to Fig. 3.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 17306-17313) copyright 2007.

Figures were selected by the author.

Author's comment

The human lung cytochrome P450 2A13 (CYP2A13) activates the nicotine-derived procarcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) into DNA-altering compounds that cause lung cancer. Although CYP2A13 is 93.5% identical to the human liver cytochrome P450 2A6, CYP2A13 metabolizes NNK with much lower Km values than does CYP2A6. To investigate the structural differences between these two enzymes the structure of CYP2A13 was determined to 2.35 Å and compared to structures of CYP2A6. As expected, the overall CYP2A13 and CYP2A6 structures are very similar with an average r.m.s. deviation of 0.5 Å for the Cα atoms. Like CYP2A6, the CYP2A13 active site cavity is small and highly hydrophobic with a cluster of Phe residues composing the active site roof. Active site residue N297 is positioned to hydrogen bond with an adventitious ligand, identified as indole. Amino acid differences between CYP2A6 and CYP2A13 at positions 117, 300, 301, and 208 relate to different orientations of the ligand plane in the two protein structures and may underlie the significant variations observed in binding and catalysis of many CYP2A ligands. In addition, docking studies suggest that residues 365 and 366 may also contribute to differences in NNK metabolism.
Emily Scott, Ph.D.