PDBsum entry 2pgf

Hydrolase

PDB id: 2pgf

Contents

Protein chain

359 a.a. *

Ligands

ADN

CCN ×2

Metals

_ZN

Waters ×248

* Residue conservation analysis

PDB id:

2pgf

Name:

Hydrolase

Title:

Crystal structure of adenosine deaminase from plasmodium vivax in complex with adenosine

Structure:

Adenosine deaminase. Chain: a. Engineered: yes

Source:

Plasmodium vivax. Malaria parasite p. Vivax. Organism_taxid: 5855. Gene: pv111245. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.89Å R-factor: 0.159 R-free: 0.201

Authors:

E.T.Larson,E.A.Merritt,Structural Genomics Of Pathogenic Protozoa Consortium (Sgpp)

Key ref:

E.T.Larson et al. (2008). Structures of substrate- and inhibitor-bound adenosine deaminase from a human malaria parasite show a dramatic conformational change and shed light on drug selectivity. J Mol Biol, 381, 975-988. PubMed id: 18602399 DOI: 10.1016/j.jmb.2008.06.048

Date:

09-Apr-07 Release date: 24-Apr-07

Protein chain

A5KE01  (A5KE01_PLAVS) -  Adenosine deaminase from Plasmodium vivax (strain Salvador I)

Seq: 363 a.a.

Struc: 359 a.a.

Enzyme reactions

• Enzyme class 1: E.C.3.5.4.31 - S-methyl-5'-thioadenosine deaminase.
• Reaction: S-methyl-5'-thioadenosine + H2O + H⁺ = S-methyl-5'-thioinosine + NH4⁺

S-methyl-5'-thioadenosine + H2O + H(+) (Bound ligand (Het Group name = ADN) matches with 85.71% similarity) = S-methyl-5'-thioinosine + NH4(+)

• Enzyme class 2: E.C.3.5.4.4 - adenosine deaminase.
• Reaction:
  1. adenosine + H2O + H⁺ = inosine + NH4⁺
  2. 2'-deoxyadenosine + H2O + H⁺ = 2'-deoxyinosine + NH4⁺

adenosine (Bound ligand (Het Group name = ADN) corresponds exactly) + H2O + H(+) = inosine + NH4(+)

2'-deoxyadenosine (Bound ligand (Het Group name = ADN) matches with 94.74% similarity) + H2O + H(+) = 2'-deoxyinosine + NH4(+)

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: 10.1016/j.jmb.2008.06.048

J Mol Biol 381:975-988 (2008)

PubMed id: 18602399

Structures of substrate- and inhibitor-bound adenosine deaminase from a human malaria parasite show a dramatic conformational change and shed light on drug selectivity.

E.T.Larson, W.Deng, B.E.Krumm, A.Napuli, N.Mueller, W.C.Van Voorhis, F.S.Buckner, E.Fan, A.Lauricella, G.DeTitta, J.Luft, F.Zucker, W.G.Hol, C.L.Verlinde, E.A.Merritt.

ABSTRACT

Plasmodium and other apicomplexan parasites are deficient in purine biosynthesis, relying instead on the salvage of purines from their host environment. Therefore, interference with the purine salvage pathway is an attractive therapeutic target. The plasmodial enzyme adenosine deaminase (ADA) plays a central role in purine salvage and, unlike mammalian ADA homologs, has a further secondary role in methylthiopurine recycling. For this reason, plasmodial ADA accepts a wider range of substrates, as it is responsible for deamination of both adenosine and 5'-methylthioadenosine. The latter substrate is not accepted by mammalian ADA homologs. The structural basis for this natural difference in specificity between plasmodial and mammalian ADA has not been well understood. We now report crystal structures of Plasmodium vivax ADA in complex with adenosine, guanosine, and the picomolar inhibitor 2'-deoxycoformycin. These structures highlight a drastic conformational change in plasmodial ADA upon substrate binding that has not been observed for mammalian ADA enzymes. Further, these complexes illuminate the structural basis for the differential substrate specificity and potential drug selectivity between mammalian and parasite enzymes.

Selected figure(s)

Figure 4.
Fig. 4. The boot-shaped active-site cavity and putative ammonium channel gate of the active conformation of plasmodial ADA. (a) Side view of the cavity, looking into the side opposite the catalytic zinc. The enclosed adenosine and DCF (yellow and orange sticks, respectively) and water molecules (red spheres) that occupy the cavity are displayed. The catalytic zinc (magenta spheres) makes up one wall of the “heel” of the boot. (b) The view has been rotated − 100° along the y-axis and is now into the “toe” of the boot. Note that the hydroxyl group of DCF that is equivalent to the leaving amine group of adenosine is oriented toward the putative ammonium channel. (c) The ammonia channel gate. Conformational changes in α13 and in the side chain of Asp205 exist between the closed, substrate-bound (d) and open, apo (e) forms of ADA. In the closed form, the solvent-filled channel leading to the surface from the active site is blocked by the side chain of Asp205. When the enzyme is not bound to ligand, the Asp205 side chain adopts an alternate conformation that allows the channel access to the surrounding solvent, presumably facilitating the release of the ammonia product.

Figure 6.
Fig. 6. (a and b) Alternate sugar pucker of substrate/inhibitor induced by the plasmodial ADA Asp172:mammalian ADA Met155 sequence difference. Plasmodial ADA is cyan and its bound DCF in orange, while mammalian ADA is green and its bound DCF in pink. Plasmodial ADA Asp172 hydrogen-bonds with the ribose 3′-hydroxyl group, an interaction that mammalian Met155 is incapable of making. This causes the plasmodial ADA-bound inhibitor to adopt a C2′-endo sugar pucker, while the mammalian ADA-bound inhibitor adopts a C4′-exo pucker. The result is that the 5′-carbon of the two riboses are oriented significantly differently with respect to the ribose ring, although the 5′-hydroxyl groups occupy nearly the same location and are less than 0.4 Å apart. The different orientations of the 5′-carbon, however, has a great affect on the space that additions at this position may occupy, while maintaining a biologically relevant glycosidic linkage with the purine ring. (c) Stereo view of 5′-PhS-DCF (purple sticks) docked into the active-site cavity of plasmodial ADA and superimposed on the crystallographically observed DCF (orange sticks). The plasmodial ADA crystal structure is cyan, while the protein following docking is green. The most significant change in the structure of plasmodial ADA in order to accommodate the 5′-thiophenyl addition is an alternate rotamer adopted by Phe132, which both enlarges the cavity and stabilizes the 5′ addition.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 381, 975-988) copyright 2008.

Figures were selected by an automated process.