PDBsum entry: 1byr

Endonuclease

PDB id: 1byr

Contents

Protein chain

152 a.a. *

Waters ×188

* Residue conservation analysis

PDB id:

1byr

Name:

Endonuclease

Title:

Crystal structure of a phospholipase d family member, nuc fr salmonella typhimurium

Structure:

Protein (endonuclease). Chain: a. Engineered: yes

Source:

Salmonella typhimurium. Organism_taxid: 602. Cellular_location: periplasm. Gene: nuc. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Homo-Dimer (from PDB file)

Resolution:

2.00Å R-factor: 0.193 R-free: 0.250

Authors:

J.A.Stuckey,J.E.Dixon

Key ref:

J.A.Stuckey and J.E.Dixon (1999). Crystal structure of a phospholipase D family member. Nat Struct Biol, 6, 278-284. PubMed id: 10074947 DOI: 10.1038/6716

Date:

19-Oct-98 Release date: 19-Oct-99

Protein chain

Q46707  (Q46707_ECOLX) -  Endonuclease

Seq: 177 a.a.

Struc: 152 a.a.

 Gene Ontology (GO) functional annotation 

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

DOI no: 10.1038/6716

Nat Struct Biol 6:278-284 (1999)

PubMed id: 10074947

Crystal structure of a phospholipase D family member.

J.A.Stuckey, J.E.Dixon.

ABSTRACT

The first crystal structure of a phospholipase D (PLD) family member has been determined at 2.0 A resolution. The PLD superfamily is defined by a common sequence motif, HxK(x)4D(x)6GSxN, and includes enzymes involved in signal transduction, lipid biosynthesis, endonucleases and open reading frames in pathogenic viruses and bacteria. The crystal structure suggests that residues from two sequence motifs form a single active site. A histidine residue from one motif acts as a nucleophile in the catalytic mechanism, forming a phosphoenzyme intermediate, whereas a histidine residue from the other motif appears to function as a general acid in the cleavage of the phosphodiester bond. The structure suggests that the conserved lysine residues are involved in phosphate binding. Large-scale genomic sequencing revealed that there are many PLD family members. Our results suggest that all of these proteins may possess a common structure and catalytic mechanism.

Selected figure(s)

Figure 1.
Figure 1. Domain organization of the PLD superfamily of phosphodiesterases. a, Nuc is the smallest member of the PLD family containing only one catalytic domain (yellow box). The YMT (Yersinia murine toxin isolated from Yersinia pestis^26) and HPLD (human PLD1)^27 proteins both contain two domains (yellow and purple boxes, respectively). Each domain harbors one consensus sequence (white box). b, The proposed catalytically active form of Nuc is depicted as a MOLSCRIPT^28 ribbon diagram (monomer A in yellow, monomer B in purple, and the variable loop in red). The arrows and coils represent -strands and -helices, respectively. The N- and C-termini are marked as N and C, respectively. The C atoms of the consensus sequence residues are drawn as cpk models with the following color scheme: histidine (green), lysine (dark blue), aspartic acid (red), serine (orange), and asparagine (cyan). c, A stereo diagram depicting a monomer of Nuc as a C -trace. The C atoms of the 153 residues are shown as spheres, with several labeled with their corresponding residue numbers. The N and C labels designate the N- and C-termini, respectively. d, Stereo diagram of two -strands, residues 52−61 (left side) and residues 82−88 (right side), are shown with the refined 2F[o] - F[c] electron density map (gray grid) contoured at 2 . Protein atoms are shown as balls and sticks with carbons in yellow, nitrogens in blue and oxygens in red.

Figure 4.
Figure 4. The two-step catalytic mechanism of the PLD superfamily of phosphodiesterases. The histidine residues are expected to play two different roles in the reaction pathway. The first step of the reaction depicts the imidazole nitrogen from His 94 in monomer A (His[A] 94) as the nucleophile that attacks the phosphorus atom of the substrate, while the histidine from monomer B (His[B] 94) is shown as the general acid donating a hydrogen to the OR' leaving group. The phosphoenzyme intermediate formed in the first step is hydrolyzed by an activated water molecule in the second step. It is conceivable that the water molecule can be replaced with other compounds specific to each family member. In the case of phosphatidylserine synthase, a serine activated by His[B] 94 would most likely hydrolyze the intermediate. The glutamic acids, which hydrogen-bond to the histidines in the crystal structure, may function to lower the effective pK[a] of each histidine and stabilize their different ionic forms in the reaction pathway.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (1999, 6, 278-284) copyright 1999.

Figures were selected by an automated process.