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

PDB id:

1jdv

Name:

Transferase

Title:

Crystal structure of 5'-deoxy-5'-methylthioadenosine phosphorylase complexed with adenosine and sulfate ion

Structure:

5'-methylthioadenosine phosphorylase. Chain: a, b, c, d, e, f. Synonym: mta phosphorylase. Mtap. Engineered: yes

Source:

Sulfolobus solfataricus. Organism_taxid: 2287. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Hexamer (from PQS)

Resolution:

2.00Å R-factor: 0.218 R-free: 0.246

Authors:

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

Key ref:

T.C.Appleby et al. (2001). Three-dimensional structure of a hyperthermophilic 5'-deoxy-5'-methylthioadenosine phosphorylase from Sulfolobus solfataricus. J Biol Chem, 276, 39232-39242. PubMed id: 11489901 DOI: 10.1074/jbc.M105694200

Date:

15-Jun-01 Release date: 26-Oct-01

Protein chains

P50389  (PNPH_SULSO) -  Purine nucleoside phosphorylase from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

Seq: 236 a.a.

Struc: 227 a.a.

Enzyme reactions

• Enzyme class 2: E.C.2.4.2.1 - purine-nucleoside phosphorylase.
• Reaction:
  1. a purine D-ribonucleoside + phosphate = a purine nucleobase + alpha- D-ribose 1-phosphate
  2. a purine 2'-deoxy-D-ribonucleoside + phosphate = a purine nucleobase + 2-deoxy-alpha-D-ribose 1-phosphate
• Enzyme class 3: E.C.2.4.2.28 - S-methyl-5'-thioadenosine phosphorylase.
• Reaction: S-methyl-5'-thioadenosine + phosphate = 5-(methylsulfanyl)-alpha-D-ribose 1-phosphate + adenine

S-methyl-5'-thioadenosine + phosphate (Bound ligand (Het Group name = ADN) matches with 85.71% similarity) = 5-(methylsulfanyl)-alpha-D-ribose 1-phosphate + adenine

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: 10.1074/jbc.M105694200

J Biol Chem 276:39232-39242 (2001)

PubMed id: 11489901

Three-dimensional structure of a hyperthermophilic 5'-deoxy-5'-methylthioadenosine phosphorylase from Sulfolobus solfataricus.

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

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.

Selected figure(s)

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.

Figures were selected by an automated process.