PDBsum entry: 1f0i

Hydrolase

PDB id: 1f0i

Contents

Protein chain

496 a.a. *

Ligands

PO4 ×2

Waters ×699

* Residue conservation analysis

PDB id:

1f0i

Name:

Hydrolase

Title:

The first crystal structure of a phospholipase d

Structure:

Phospholipase d. Chain: a. Ec: 3.1.4.4

Source:

Streptomyces sp.. Organism_taxid: 172564. Strain: pmf

Resolution:

1.40Å R-factor: 0.130 R-free: 0.185

Authors:

I.Leiros,F.Secundo,C.Zambonelli,S.Servi,E.Hough

Key ref:

I.Leiros et al. (2000). The first crystal structure of a phospholipase D. Structure, 8, 655-667. PubMed id: 10873862 DOI: 10.1016/S0969-2126(00)00150-7

Date:

16-May-00 Release date: 16-May-01

Protein chain

P84147  (P84147_STRSM) -  Phospholipase D

Seq: 506 a.a.

Struc: 496 a.a.*

* PDB and UniProt seqs differ at 6 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.1.4.4 - Phospholipase D.
• Reaction: A phosphatidylcholine + H₂O = choline + a phosphatidate

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

 Gene Ontology (GO) functional annotation 

• Biological process: metabolic process (1 term)
• Biochemical function: catalytic activity (3 terms)

reference

DOI no: 10.1016/S0969-2126(00)00150-7

Structure 8:655-667 (2000)

PubMed id: 10873862

The first crystal structure of a phospholipase D.

I.Leiros, F.Secundo, C.Zambonelli, S.Servi, E.Hough.

ABSTRACT

BACKGROUND: The phospholipase D (PLD) superfamily includes enzymes that are involved in phospholipid metabolism, nucleases, toxins and virus envelope proteins of unknown function. PLD hydrolyzes the terminal phosphodiester bond of phospholipids to phosphatidic acid and a hydrophilic constituent. Phosphatidic acid is a compound that is heavily involved in signal transduction. PLD also catalyses a transphosphatidylation reaction in the presence of phosphatidylcholine and a short-chained primary or secondary alcohol. RESULTS: The first crystal structure of a 54 kDa PLD has been determined to 1.9 A resolution using the multiwavelength anomalous dispersion (MAD) method on a single WO(4) ion and refined to 1.4 A resolution. PLD from the bacterial source Streptomyces sp. strain PMF consists of a single polypeptide chain that is folded into two domains. An active site is located at the interface between these domains. The presented structure supports the proposed superfamily relationship with the published structure of the 16 kDa endonuclease from Salmonella typhimurium. CONCLUSIONS: The structure of PLD provides insight into the structure and mode of action of not only bacterial, plant and mammalian PLDs, but also of a variety of enzymes as diverse as cardiolipin synthases, phosphatidylserine synthases, toxins, endonucleases, as well as poxvirus envelope proteins having a so far unknown function. The common features of these enzymes are that they can bind to a phosphodiester moiety, and that most of these enzymes are active as bi-lobed monomers or dimers.

Selected figure(s)

Figure 2.
Figure 2. Topology and tertiary structure of PLD. (a) Overall topology of PLD from Streptomyces sp. strain PMF. Modified figure from TOPS [46]. The N-terminal 260 residues are shown in light blue and the remainder of the protein is colored in dark blue, in order to separate the two domains. (b) Stereographic overview of the tertiary arrangement of the protein. Helices are shown in red and strands in yellow. The protein is viewed from the outer membrane, and the active-site-bound phosphate can be seen in the center of the protein. This Figure was created using BOBSCRIPT. (c) Stereographic presentation of the Ca trace of PLD, made using BOBSCRIPT. The orientation of the protein is as in (b).

The above figure is reprinted by permission from Cell Press: Structure (2000, 8, 655-667) copyright 2000.

Figure was selected by an automated process.