PDBsum entry 1s1d

Hydrolase

PDB id: 1s1d

Contents

Protein chain

317 a.a. *

Ligands

ACT

GP2 ×2

TRS ×7

SO4 ×2

Metals

_CA ×2

Waters ×650

* Residue conservation analysis

PDB id:

1s1d

Name:

Hydrolase

Title:

Structure and protein design of human apyrase

Structure:

Apyrase. Chain: a, b. Synonym: ca2+-dependent endoplasmic reticulum nucleoside diphosphatase. Apyrase. Soluble calcium-activated nucleotidase scan- 1. Engineered: yes

Source:

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

Resolution:

1.60Å R-factor: 0.166 R-free: 0.194

Authors:

J.Dai,J.Liu,Y.Deng,T.M.Smith,M.Lu

Key ref:

J.Dai et al. (2004). Structure and protein design of a human platelet function inhibitor. Cell, 116, 649-659. PubMed id: 15006348 DOI: 10.1016/S0092-8674(04)00172-2

Date:

06-Jan-04 Release date: 16-Mar-04

Protein chains

Q8WVQ1  (CANT1_HUMAN) -  Soluble calcium-activated nucleotidase 1 from Homo sapiens

Seq: 401 a.a.

Struc: 317 a.a.

Enzyme reactions

• Enzyme class: E.C.3.6.1.6 - nucleoside diphosphate phosphatase.
• Reaction: a ribonucleoside 5'-diphosphate + H2O = a ribonucleoside 5'-phosphate + phosphate + H⁺

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

Key reference

DOI no: 10.1016/S0092-8674(04)00172-2

Cell 116:649-659 (2004)

PubMed id: 15006348

Structure and protein design of a human platelet function inhibitor.

J.Dai, J.Liu, Y.Deng, T.M.Smith, M.Lu.

ABSTRACT

Hematophagous arthropods secrete a salivary apyrase that inhibits platelet activation by catabolizing ADP released from damaged tissues and blood cells. We report the X-ray crystal structures of a human enzyme of the soluble apyrase family in its apo state and bound to a substrate analog. The structures reveal a nucleotide binding domain comprising a five-blade beta propeller, binding determinants of the substrate and the active site, and an unusual calcium binding site with a potential regulatory function. Using a comparative structural biology approach, we were able to redesign the human apyrase so as to enhance its ADPase activity by more than 100-fold. The engineered enzyme is a potent inhibitor of platelet aggregation and may serve as the basis for the development of a new class of antithrombotic agents.

Selected figure(s)

Figure 1.
Figure 1. Structure of Apo Human ApyraseRibbon diagram of the human apyrase propeller structure as viewed along (A) or perpendicular to (B) the central tunnel. The sheets are numbered 1 to 5 and organized sequentially in a counterclockwise direction, and the four antiparallel β strands within each sheet are denoted a to d in the order from axis to perimeter. The β propeller is circularized by juxtaposition of the 1a and 1b strands. The polypeptide chain is colored from blue at the N terminus through to red at the C terminus. The Ca^2+ ion (green sphere) is located in the middle of the central tunnel.(C) Superposition of the α carbon traces of the five blades of the human apyrase propeller. Blades 2 and 5 (green and light blue) have the shortest loops between β strands. Blades 1, 3, and 4 (gray, yellow, and pink) have at least one long loop projecting from the top face of the β propeller.(D) Stereoview of the 2F[o] − F[c] electron density map (contoured at 1.5σ) showing the coordination geometry of the Ca^2+ ion (green sphere) connecting the five blades of the human apyrase propeller. Water molecules are shown as red spheres, and calcium coordinations are denoted by dotted lines.(E) Sequence alignment of the five blades of the human apyrase propeller. The approximate boundaries of the β strands are highlighted. φ designates conserved hydrophobic residues.

Figure 2.
Figure 2. Structure-Based Alignment of Human Apyrase with Other Apyrase ProteinsThe sequence of human apyrase (residues Pro1–Ile333) is shown with the elements of secondary structure indicated above the alignment. Gray arrows and cylinders mark β strands and α helices, respectively, with crosses denoting residues that are disordered in the present apo and substrate analog structures. The sequences of human, rat, bed bug, and sand fly (Phlebotomus) are shown; in these cases the enzymatic activity has been established by biochemical analysis. Residues that are important for nucleotide and Ca^2+ binding are indicated by pluses and asterisks, respectively. Chemically similar residues in the apyrase family are colored red and residues conserved in the vertebrate and insect subfamilies in blue and green, respectively. We refer to the human apyrase structure using the numbering system of the mature protein.

The above figures are reprinted by permission from Cell Press: Cell (2004, 116, 649-659) copyright 2004.

Figures were selected by an automated process.