PDBsum entry: 1u9z

Transferase

PDB id: 1u9z

Contents

Protein chains

274 a.a. *

Ligands

R5P ×4

AMP ×4

Waters ×206

* Residue conservation analysis

PDB id:

1u9z

Name:

Transferase

Title:

Crystal structure of phosphoribosyl diphosphate synthase complexed with amp and ribose 5-phosphate

Structure:

Ribose-phosphate pyrophosphokinase. Chain: a, b, c, d. Fragment: phosphoribosyl diphosphate synthase. Synonym: phosphoribosyl diphosphate synthase. Rppk. Phosphoribosyl pyrophosphate synthetase. P-rib-pp synthetase. Prpp synthetase. Engineered: yes

Source:

Methanocaldococcus jannaschii. Organism_taxid: 2190. Gene: prs. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Tetramer (from PQS)

Resolution:

2.80Å R-factor: 0.238 R-free: 0.272

Authors:

A.Kadziola,E.Johansson,C.H.Jepsen,J.Mcguire,S.Larsen,B.Hove- Jensen

Key ref:

A.Kadziola et al. (2005). Novel class III phosphoribosyl diphosphate synthase: structure and properties of the tetrameric, phosphate-activated, non-allosterically inhibited enzyme from Methanocaldococcus jannaschii. J Mol Biol, 354, 815-828. PubMed id: 16288921 DOI: 10.1016/j.jmb.2005.10.001

Date:

11-Aug-04 Release date: 23-Aug-05

Protein chains

Q58761  (KPRS_METJA) -  Ribose-phosphate pyrophosphokinase

Seq: 284 a.a.

Struc: 274 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.6.1 - Ribose-phosphate diphosphokinase.
• Pathway: Ribose activation
• Reaction: ATP + D-ribose 5-phosphate = AMP + 5-phospho-alpha-D-ribose 1-diphosphate

ATP + D-ribose 5-phosphate (Bound ligand (Het Group name = R5P) corresponds exactly) = AMP (Bound ligand (Het Group name = AMP) corresponds exactly) + 5-phospho-alpha-D-ribose 1-diphosphate

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

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: nucleoside metabolic process (2 terms)
• Biochemical function: nucleotide binding (7 terms)

reference

DOI no: 10.1016/j.jmb.2005.10.001

J Mol Biol 354:815-828 (2005)

PubMed id: 16288921

Novel class III phosphoribosyl diphosphate synthase: structure and properties of the tetrameric, phosphate-activated, non-allosterically inhibited enzyme from Methanocaldococcus jannaschii.

A.Kadziola, C.H.Jepsen, E.Johansson, J.McGuire, S.Larsen, B.Hove-Jensen.

ABSTRACT

The prs gene encoding phosphoribosyl diphosphate (PRPP) synthase of the hyperthermophilic autotrophic methanogenic archaeon Methanocaldococcus jannaschii has been cloned and expressed in Escherichia coli. Subsequently, M.jannaschii PRPP synthase has been purified, characterised, crystallised, and the crystal structure determined. The enzyme is activated by phosphate ions and only ATP or dATP serve as diphosphoryl donors. The K(m) values are determined as 2.6 mM and 2.8 mM for ATP and ribose 5-phosphate, respectively, and the V(max) value as 2.20 mmol (minxmg of protein)(-1). ADP is a potent inhibitor of activity while GDP has no effect. A single ADP binding site, the active site, is present per subunit. The crystal structure of the enzyme reveals a more compact subunit than that of the enzyme from the mesophile Bacillus subtilis, caused by truncations at the N and C terminus as well as shorter loops in the M.jannaschii enzyme. The M.jannaschii enzyme displays a tetrameric quaternary structure in contrast to the hexameric quaternary structure of B.subtilis PRPP synthase. Soaking of the crystals with 5'-AMP and PRPP revealed the position of the former compound as well as that of ribose 5-phosphate. The properties of M.jannaschii PRPP synthase differ widely from previously characterised PRPP synthases by its tetrameric quaternary structure and the simultaneous phosphate ion-activation and lack of allosteric inhibition, and, thus, constitute a novel class of PRPP synthases.

Selected figure(s)

Figure 3.
Figure 3. Stereo C^a trace of the M. jannaschii PRPP synthase subunit with the ligands ribose 5-phosphate and AMP. The active site is situated at the interface between the N and C-terminal domains which are related by pseudo 2-fold symmetry.13 The C^a trace, which has bullets every ten residues and which is numbered every 20 residues was prepared with MOLSCRIPT and Raster3D.48^ and 49 The following secondary structure elements have been assigned. b[1]: Ile2-Gly6, a[2]: Ser9-Leu20, b[3]: Arg26-Phe32, b[4]: Glu36-Val42, b[5]: Asp48-Asn54, a[6]: Asn58-Asp75, b[7]: Lys80-Ala85, a8: Ile103-Val116, b[9]: Asp117-Asn123, 3[10]: His128-Phe133, b[11]: Pro136-Gly140, a[12]: Ala142-Lys151, b[13]: Ile158-Ala161, a[14]: Leu167-Asn178, b[15]: Glu180-Glu185, b[16]: Ala197-Lys199, b[17]: Asp207-Asp213, a[18]: Gly218-Gln231, b[19]: Lys235-His242, a[20]: Asp248-Ala256, b[21]: Glu259-Val262, a[22]: Val276-Asp282.

Figure 4.
Figure 4. M. jannaschii PRPP synthase tetramer viewed along the three perpendicular 2-fold axes. The four subunits of the tetramer are displayed in red (A), green (B), magenta (C), and cyan (D). The Figure was made with MOLSCRIPT and Raster3D.48^ and 49

The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 354, 815-828) copyright 2005.

Figures were selected by an automated process.