PDBsum entry: 1rky

Oxidoreductase

PDB id: 1rky

Contents

Protein chain

735 a.a. *

Ligands

NAG ×4

NAG-NAG-BMA

IMD

Metals

_XE ×8

_CU

_CA ×2

_MG ×3

_CL ×6

Waters ×632

* Residue conservation analysis

PDB id:

1rky

Name:

Oxidoreductase

Title:

Pplo + xe

Structure:

Lysyl oxidase. Chain: a. Fragment: residues 41-787. Synonym: pplo. Engineered: yes

Source:

Pichia pastoris. Organism_taxid: 4922. Gene: atcc 28, 485. Expressed in: pichia pastoris. Expression_system_taxid: 4922.

Biol. unit:

Dimer (from PDB file)

Resolution:

1.68Å R-factor: 0.151 R-free: 0.182

Authors:

J.M.Guss,A.P.Duff

Key ref:

A.P.Duff et al. (2004). Using xenon as a probe for dioxygen-binding sites in copper amine oxidases. J Mol Biol, 344, 599-607. PubMed id: 15533431 DOI: 10.1016/j.jmb.2004.09.075

Date:

24-Nov-03 Release date: 07-Dec-04

Protein chain

Q96X16  (Q96X16_PICPA) -  Lysyl oxidase

Seq: 787 a.a.

Struc: 735 a.a.*

* PDB and UniProt seqs differ at 10 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 

• Biological process: oxidation-reduction process (2 terms)
• Biochemical function: quinone binding (4 terms)

DOI no: 10.1016/j.jmb.2004.09.075

J Mol Biol 344:599-607 (2004)

PubMed id: 15533431

Using xenon as a probe for dioxygen-binding sites in copper amine oxidases.

A.P.Duff, D.M.Trambaiolo, A.E.Cohen, P.J.Ellis, G.A.Juda, E.M.Shepard, D.B.Langley, D.M.Dooley, H.C.Freeman, J.M.Guss.

ABSTRACT

Potential dioxygen-binding sites in three Cu amine oxidases have been investigated by recording X-ray diffraction data at 1.7-2.2A resolution for crystals under a high pressure of xenon gas. Electron-density difference maps and crystallographic refinement provide unequivocal evidence for a number of Xe-binding sites in each enzyme. Only one of these sites is present in all three Cu amine oxidases studied. Structural changes elsewhere in the protein molecules are insignificant. The results illustrate the use of xenon as a probe for cavities, in which a protein may accommodate a dioxygen molecule. The finding of a potential dioxygen-binding cavity close to the active site of Cu amine oxidases may be relevant to the function of the enzymes, since the formation of a transient protein-dioxygen complex is a likely step in the catalytic mechanism. No evidence was found for xenon binding in a region of the molecule that was previously identified in two other Cu amine oxidases as a potential transient dioxygen-binding site.

Selected figure(s)

Figure 1.
Figure 1. Electron density at the active-site Xe atom in Xe-AGAO. Gray contours: (2F[obs] -F[calc]) density plotted at 2s(r). Purple contours: anomalous density plotted at 6s(r), showing the positions of the Xe (gold) and Cu (cyan) atoms. In the crystal structure of native AGAO, there is no electron or anomalous density at the position of the Xe atom.

Figure 3.
Figure 3. The Xe site closest to the TPQ cofactor and Cu atom in the structures of Xe-AGAO, Xe-PPLO and Xe-PSAO, and in models of Xe-HPAO and Xe-ECAO. Small spheres represent the Xe atom (gold) and the Cu atom (cyan). Water molecules are not shown. Labels indicate the nearest-neighbor residues of each Xe atom. In the models of Xe-HPAO and Xe-ECAO, the position of the Xe atom was optimized by using CNS39 to minimize the repulsive van der Waals energy. (a) Xe-AGAO. In the Xe-AGAO complex, the side-chain of Leu590 occurs as two rotamers. The rotamer shown here is consistent with the presence of the Xe atom. The other rotamer would conflict with the Xe atom. (b) Xe-PPLO. The conformation of Leu692 shown in the Figure is one of two conformations observed in the native protein (A.P.D., unpublished results). Only this conformation is sterically acceptable when Xe is bound. (c) Xe-PSAO. Three side-chains in the Xe complex have a conformation different from that in native PSAO. The side-chains of Leu407, Ile601 and Thr618 are rotated about C^a-C^b by vert, similar 45°, vert, similar 160° and vert, similar 130°, respectively. (d) Xe-HPAO (model). The modeled Xe site in HPAO closely resembles the actual site in PSAO. In order to accommodate a Xe atom, the side-chains of Leu425 and Ile639 were rotated from their positions (yellow) in the native protein [1a2v],30 until they superposed closely on the homologous residues Leu407 and Thr618 in PSAO. In Leu425 the required rotations were vert, similar 50° about C^a-C^b, and vert, similar 10° about C^b-C^g; in Ile639 they were vert, similar 80° about C^a-C^b, and vert, similar 10°about C^b-C^g1. The position of the Xe atom was then optimized (see above). (e) Xe-ECAO (model). In native ECAO (1oac)31 this cavity is occupied by two water molecules, one of which makes a 2.6 Å O three dots, centered O contact (i.e. an O three dots, centered H-O bond) with the side-chain of Tyr528. The Xe site was modeled by removing the water molecules, inserting a Xe atom, and optimizing the position of the Xe atom (see above). In the resulting model, the Xe position is vert, similar 1 Å from the mid-point of the two displaced water molecules. The closest contact with Tyr528 is 3.7 Å (Table 2A).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 344, 599-607) copyright 2004.

Figures were selected by an automated process.