PDBsum entry 1i5e

Transferase

PDB id: 1i5e

Contents

Protein chains

208 a.a. *

Ligands

U5P ×2

Waters ×2

* Residue conservation analysis

PDB id:

1i5e

Name:

Transferase

Title:

Crystal structure of bacillus caldolyticus uracil phosphoribosyltransferase with bound ump

Structure:

Uracil phosphoribosyltransferase. Chain: a, b. Synonym: ump pyrophosphorylase. Engineered: yes

Source:

Bacillus caldolyticus. Organism_taxid: 1394. Gene: upp. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

3.00Å R-factor: 0.223 R-free: 0.270

Authors:

A.Kadziola,J.Neuhard,S.Larsen

Key ref:

A.Kadziola et al. (2002). Structure of product-bound Bacillus caldolyticus uracil phosphoribosyltransferase confirms ordered sequential substrate binding. Acta Crystallogr D Biol Crystallogr, 58, 936-945. PubMed id: 12037295 DOI: 10.1107/S0907444902005024

Date:

27-Feb-01 Release date: 05-Jun-02

Protein chains

P70881  (UPP_BACCL) -  Uracil phosphoribosyltransferase from Bacillus caldolyticus

Seq: 209 a.a.

Struc: 208 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.4.2.9 - uracil phosphoribosyltransferase.
• Reaction: UMP + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + uracil

UMP + diphosphate (Bound ligand (Het Group name = U5P) corresponds exactly) = 5-phospho-alpha-D-ribose 1-diphosphate + uracil

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

reference

DOI no: 10.1107/S0907444902005024

Acta Crystallogr D Biol Crystallogr 58:936-945 (2002)

PubMed id: 12037295

Structure of product-bound Bacillus caldolyticus uracil phosphoribosyltransferase confirms ordered sequential substrate binding.

A.Kadziola, J.Neuhard, S.Larsen.

ABSTRACT

Uracil phosphoribosyltransferase (UPRTase) is part of the salvage pathway that leads to the biosynthesis of UMP. It catalyzes the formation of UMP and pyrophosphate from uracil and alpha-D-5-phosphoribosyl-1-pyrophosphate. Unlike enzymes in the de novo synthesis of UMP, UPRTases have only been found in lower organisms and are therefore potential targets for the development of new antibiotics. UPRTase from Bacillus caldolyticus has been crystallized and the structure has been determined by isomorphous replacement and refined to 3.0 A resolution. UPRTase from B. caldolyticus forms a dimer with the active sites pointing away from each other. A long arm from each subunit wraps around the other subunit, contributing half of the dimer interface. The monomer adopts the phosphoribosyltransferase type I fold, with a small C-terminal hood defining the uracil-binding site. The structure contains a well defined UMP molecule in the active site. The binding of UMP involves two sequence segments that are highly conserved among UPRTases. The first segment, Asp131-Ser139, contains the PRPP-binding consensus sequence motif known from other type I phosphoribosyltransferases and binds the ribose-5'-phosphate part of UMP. The second segment, Tyr193-Ala201, which is specific for uracil phosphoribosyltransferases, binds the uracil part of UMP through backbone contacts, partly mediated by a water molecule. Modelling of a PRPP-enzyme complex reveals that uracil can be activated to its tautomeric enol form by the complex. This is consistent with kinetic data, which display ordered sequential binding of substrates, with PRPP binding first. Based on this observation, a reaction mechanism is proposed.

Selected figure(s)

Figure 7.
Figure 7 Stereoview of a hypothetical enzyme-substrate complex. The substrate molecules uracil and PRPP are shown (black bonds) superposed onto the actual enzyme-product complex (white bonds) for which the structure was determined. The ribose-5'-phosphate part common to substrate and product has grey bonds.

Figure 8.
Figure 8 Proposed catalytic mechanism for uracil phosphoribosyltransferase: when PRPP is bound to the enzyme and uracil enters the active site (Fig. 7-), uracil is stabilized as the enol tautomer. When in the enol form, uracil enters deeper into the active site and the shown electron translocation takes place, completing the reaction.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2002, 58, 936-945) copyright 2002.

Figures were selected by the author.