PDBsum entry 1vch

Transferase

PDB id: 1vch

Contents

Protein chains

169 a.a. *

152 a.a. *

Ligands

ACY ×4

Metals

_CL ×5

_CA

Waters ×373

* Residue conservation analysis

PDB id:

1vch

Name:

Transferase

Title:

Crystal structure of a phosphoribosyltransferase-related protein from thermus thermophilus

Structure:

Phosphoribosyltransferase-related protein. Chain: a, b, c, d, e. Engineered: yes

Source:

Thermus thermophilus. Organism_taxid: 274. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PDB file)

Resolution:

1.94Å R-factor: 0.232 R-free: 0.259

Authors:

P.H.Rehse,T.H.Tahirov,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

P.H.Rehse and T.H.Tahirov (2005). Crystal structure of a purine/pyrimidine phosphoribosyltransferase-related protein from Thermus thermophilus HB8. Proteins, 61, 658-665. PubMed id: 16152602 DOI: 10.1002/prot.20624

Date:

08-Mar-04 Release date: 22-Mar-05

Protein chains

Q5SHW7  (Q5SHW7_THET8) -  Adenine phosphoribosyltransferase from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 175 a.a.

Struc: 169 a.a.

Protein chain

Q5SHW7  (Q5SHW7_THET8) -  Adenine phosphoribosyltransferase from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 175 a.a.

Struc: 152 a.a.

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E: E.C.2.4.2.7 - adenine phosphoribosyltransferase.
• Pathway: Ribose activation
• Reaction: AMP + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + adenine

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

reference

DOI no: 10.1002/prot.20624

Proteins 61:658-665 (2005)

PubMed id: 16152602

Crystal structure of a purine/pyrimidine phosphoribosyltransferase-related protein from Thermus thermophilus HB8.

P.H.Rehse, T.H.Tahirov.

ABSTRACT

Adenine phosphoribosyltransferase (APRTase) is a widely distributed enzyme involved in the salvage of adenine to form an adenine nucleotide. We crystallized and determined the X-ray crystallographic structure of a purine/pyrimidine phosphoribosyltransferase-related protein from the thermophilic bacterium, Thermus thermophilus HB8. The crystal space group was C2 with unit cell dimensions of a = 167.42 A, b = 61.41 A, c = 102.39 A, beta = 94.0 degrees . Initial phases were determined to 2.6 A using the multiple wavelength anomalous dispersion method and selenomethionine substituted protein (Se-MAD), and refined using a 1.9 A "native" data set. The asymmetric unit contains two pairs of identical dimers, each related by noncrystallographic two-fold symmetry. The fifth monomer forms a similar dimer across a crystallographic two-fold axis. These dimers appear to be the biological unit with both monomers contributing to an unusual highly charged arginine-rich bridge region separating the two active sites. Comparison with distantly related APRTases reveal similarities and differences of the active site.

Selected figure(s)

Figure 3.
Figure 3. (a) Stereo view of the biological unit. (b) Electrostatic potential surface of TtAPRTase. (c) Electrostatic potential surface of human APRTase.Both (a) and (b) are oriented to display the arginine-rich bridging region of the TtAPRTase. The AMP is modeled into the TtAPRTase.

Figure 4.
Figure 4. (a) Active site including the arginine-rich region created by the two-fold axis. The modeled AMP is in blue; the A chain is in black, and the B chain is in red. (b) Selected active site residues from the T. thermophilus (yellow) and human (red) APRTases. AMP is in blue.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2005, 61, 658-665) copyright 2005.

Figures were selected by an automated process.