PDBsum entry 1jdv

Transferase

PDB id: 1jdv

Contents

Protein chains

(+ 0 more) 227 a.a. *

Ligands

SO4 ×6

ADN ×4

Waters ×304

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Three-Dimensional structure of a hyperthermophilic 5'-Deoxy-5'-Methylthioadenosine phosphorylase from sulfolobus solfataricus.

Authors

T.C.Appleby, I.I.Mathews, M.Porcelli, G.Cacciapuoti, S.E.Ealick.

Ref.

J Biol Chem, 2001, 276, 39232-39242. [DOI no: 10.1074/jbc.M105694200]

PubMed id

11489901

Abstract

The structure of 5'-deoxy-5'-methylthioadenosine phosphorylase from Sulfolobus solfataricus (SsMTAP) has been determined alone, as ternary complexes with sulfate plus substrates 5'-deoxy-5'-methylthioadenosine, adenosine, or guanosine, or with the noncleavable substrate analog Formycin B and as binary complexes with phosphate or sulfate alone. The structure of unliganded SsMTAP was refined at 2.5-A resolution and the structures of the complexes were refined at resolutions ranging from 1.6 to 2.0 A. SsMTAP is unusual both for its broad substrate specificity and for its extreme thermal stability. The hexameric structure of SsMTAP is similar to that of purine-nucleoside phosphorylase (PNP) from Escherichia coli, however, only SsMTAP accepts 5'-deoxy-5'-methylthioadenosine as a substrate. The active site of SsMTAP is similar to that of E. coli PNP with 13 of 18 nearest residues being identical. The main differences are at Thr(89), which corresponds to serine in E. coli PNP, and Glu(163), which corresponds to proline in E. coli PNP. In addition, a water molecule is found near the purine N-7 position in the guanosine complex of SsMTAP. Thr(89) is near the 5'-position of the nucleoside and may account for the ability of SsMTAP to accept either hydrophobic or hydrophilic substituents in that position. Unlike E. coli PNP, the structures of SsMTAP reveal a substrate-induced conformational change involving Glu(163). This residue is located at the interface between subunits and swings in toward the active site upon nucleoside binding. The high-resolution structures of SsMTAP suggest that the transition state is stabilized in different ways for 6-amino versus 6-oxo substrates. SsMTAP has optimal activity at 120 degrees C and retains full activity after 2 h at 100 degrees C. Examination of the three-dimensional structure of SsMTAP suggests that unlike most thermophilic enzymes, disulfide linkages play a key in role in its thermal stability.

Figure 5.
Fig. 5. Active site drawing of the phosphate-binding site. a, interaction observed when sulfate occupies the site. b, interactions observed when phosphate occupies the binding site. The molecule of Tris is observed only with phosphate. Hydrogen bonds are shown as dashed lines with the corresponding donor-acceptor distance labeled. Residues belongs to the neighboring subunit are designated with an asterisk (*).

Figure 8.
Fig. 8. Active site drawing of the SsMTAP FMB-sulfate complex. a, the binding geometry for FMB. b, the binding geometry for the E. coli PNP-FMB complex for comparison. The coordinates were taken from PDB entry code 1A69 (14). Hydrogen bonds are shown as dashed lines with the corresponding donor-acceptor distance labeled. Residues belongs to the neighboring subunit are designated with an asterisk (*).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2001, 276, 39232-39242) copyright 2001.

Secondary reference #1

Title

Purification and characterization of extremely thermophilic and thermostable 5'-Methylthioadenosine phosphorylase from the archaeon sulfolobus solfataricus. Purine nucleoside phosphorylase activity and evidence for intersubunit disulfide bonds.

Authors

G.Cacciapuoti, M.Porcelli, C.Bertoldo, M.De rosa, V.Zappia.

Ref.

J Biol Chem, 1994, 269, 24762-24769.

PubMed id

7929153

Secondary reference #2

Title

Three-Dimensional structure of human erythrocytic purine nucleoside phosphorylase at 3.2 a resolution.

Authors

S.E.Ealick, S.A.Rule, D.C.Carter, T.J.Greenhough, Y.S.Babu, W.J.Cook, J.Habash, J.R.Helliwell, J.D.Stoeckler, R.E.Parks.

Ref.

J Biol Chem, 1990, 265, 1812-1820.

PubMed id

2104852

Secondary reference #3

Title

The structure of human 5'-Deoxy-5'-Methylthioadenosine phosphorylase at 1.7 a resolution provides insights into substrate binding and catalysis.

Authors

T.C.Appleby, M.D.Erion, S.E.Ealick.

Ref.

Structure, 1999, 7, 629-641. [DOI no: 10.1016/S0969-2126(99)80084-7]

PubMed id

10404592

Figure 3.
Figure 3. Stereoview of the MTAP trimer. The trimer is viewed down the molecular/crystallographic threefold axis. Each subunit is shown in a different color, with MTA and sulfate modeled in red in each of the three active sites. Broken lines indicate residues 225–229, which are missing in the final model. (The figure was produced using the program MOLSCRIPT [41].)

The above figure is reproduced from the cited reference with permission from Cell Press