PDBsum entry 1v04

Hydrolase

PDB id: 1v04

Contents

Protein chain

332 a.a. *

Ligands

PO4

Metals

_CA ×2

Waters ×115

* Residue conservation analysis

PDB id:

1v04

Name:

Hydrolase

Title:

Serum paraoxonase by directed evolution

Structure:

Serum paraoxonase/arylesterase 1. Chain: a. Synonym: a-esterase 1, serum aryldialkylphosphatase 1, pon1, aromatic esterase 1. Engineered: yes. Other_details: paraoxonase-1 (pon1)

Source:

Homo sapiens, oryctolagus cuniculus, mus musculus, rattus rattus. Organism_taxid: 9606, 9986, 10090, 10117. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: from shuffled genes of human, rabbit, mouse and rat paraoxonase

Resolution:

2.20Å R-factor: 0.186 R-free: 0.217

Authors:

M.Harel,A.Aharoni,L.Gaidukov,B.Brumshtein,O.Khersonsky,S.Yagur, R.Meged,H.Dvir,R.B.G.Ravelli,A.Mccarthy,L.Toker,I.Silman, J.L.Sussman,D.S.Tawfik

Key ref:

M.Harel et al. (2004). Structure and evolution of the serum paraoxonase family of detoxifying and anti-atherosclerotic enzymes. Nat Struct Mol Biol, 11, 412-419. PubMed id: 15098021 DOI: 10.1038/nsmb767

Date:

22-Mar-04 Release date: 23-Apr-04

Protein chain

P27170  (PON1_RABIT) -  Serum paraoxonase/arylesterase 1 from Oryctolagus cuniculus

Seq: 359 a.a.

Struc: 332 a.a.*

* PDB and UniProt seqs differ at 32 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: E.C.3.1.1.2 - arylesterase.
• Reaction: a phenyl acetate + H2O = a phenol + acetate + H⁺
• Enzyme class 2: E.C.3.1.1.81 - quorum-quenching N-acyl-homoserine lactonase.
• Reaction: an N-acyl-L-homoserine lactone + H2O = an N-acyl-L-homoserine + H⁺
• Enzyme class 3: E.C.3.1.8.1 - aryldialkylphosphatase.
• Reaction: An aryl dialkyl phosphate + H2O = dialkyl phosphate + an aryl alcohol

aryl dialkyl phosphate + H2O = dialkyl phosphate (Bound ligand (Het Group name = PO4) matches with 71.43% similarity) + aryl alcohol

• Cofactor: Divalent cation

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1038/nsmb767

Nat Struct Mol Biol 11:412-419 (2004)

PubMed id: 15098021

Structure and evolution of the serum paraoxonase family of detoxifying and anti-atherosclerotic enzymes.

M.Harel, A.Aharoni, L.Gaidukov, B.Brumshtein, O.Khersonsky, R.Meged, H.Dvir, R.B.Ravelli, A.McCarthy, L.Toker, I.Silman, J.L.Sussman, D.S.Tawfik.

ABSTRACT

Members of the serum paraoxonase (PON) family have been identified in mammals and other vertebrates, and in invertebrates. PONs exhibit a wide range of physiologically important hydrolytic activities, including drug metabolism and detoxification of nerve agents. PON1 and PON3 reside on high-density lipoprotein (HDL, 'good cholesterol') and are involved in the prevention of atherosclerosis. We describe the first crystal structure of a PON family member, a variant of PON1 obtained by directed evolution, at a resolution of 2.2 A. PON1 is a six-bladed beta-propeller with a unique active site lid that is also involved in HDL binding. The three-dimensional structure and directed evolution studies permit a detailed description of PON1's active site and catalytic mechanism, which are reminiscent of secreted phospholipase A2, and of the routes by which PON family members diverged toward different substrate and reaction selectivities.

Selected figure(s)

Figure 2.
Figure 2. PON1's active site viewed from above the propeller. (a) Central tunnel of the propeller with the two calcium atoms, and the side chains of the residues found to be mutated in the newly evolved PON1 variants for esterase and lactonase (orange) or for phosphotriesterase activity (yellow), including the R192Q human polymorphism (in the rePON1-G2E6 variant, this position is a lysine). The putative catalytic His-His dyad is red (see text and Fig. 4). (b) A surface view of the active site. Lys70, Tyr71 and Phe347 are shown as sticks to permit a better view of the active site. At the deepest point of the cavity lies the upper calcium atom (Ca1, green) to which a phosphate ion is bound.

Figure 6.
Figure 6. Proposed model for anchoring of PON1 to the surface of HDL. (a) Tertiary structure cartoon of rePON1 showing its exposed hydrophobic surfaces. N-terminal residues 7 -18, missing in the crystal structure and predicted to be helical, were modeled as part of H1. Denoted are all the hydrophobic residues (leucine, phenylalanine, proline, isoleucine, tyrosine, tryptophan and valine) appearing with accessible surface area 20 Å2. (b) Hydrophobic residues proposed to be involved in HDL anchoring (side chains yellow). The line defined by the side chains of Tyr185, Phe 186, Tyr190, Trp194, Trp202 (helix H2 and the adjacent loops) and Lys21 (helix H1) models the putative interface between HDL's hydrophobic interior and the exterior aqueous phase. The hydrophobic side chains of leucine and phenylalanine residues of H1 are primarily within the apolar region31. The active site and the selectivity-determining residues (Table 2) are blue, and the proposed glycosylation sites (Asn253 and Asn324) are red.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2004, 11, 412-419) copyright 2004.

Figures were selected by the author.