Sandbox Reserved 342
| This Sandbox is Reserved from January 10, 2010, through April 10, 2011 for use in BCMB 307-Proteins course taught by Andrea Gorrell at the University of Northern British Columbia, Prince George, BC, Canada. |
To get started:
More help: Help:Editing |
| |||||||||
| 1a96, resolution 2.00Å () | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Ligands: | , , , | ||||||||
| Gene: | GPT (Escherichia coli) | ||||||||
| Activity: | Xanthine phosphoribosyltransferase, with EC number 2.4.2.22 | ||||||||
| |||||||||
| |||||||||
| Resources: | FirstGlance, OCA, RCSB, PDBsum | ||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||
XANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASEXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
IntroductionIntroduction
Xanthine-guanine Phosphoribosyltansferase (XGPRT) is one of three purine phosphoribosyltransferases (PRTases) that are part of the purine salvage pathway in Escherichia coli[1]; the other two PRTases in the pathway are HPRT and APRT[1].
FunctionFunction
XGPRT is an enzyme that catalyzes the conversion of guanine, xanthine, and sometimes hypoxanthine, to GMP, XMP, and IMP [1]. This enzyme is part of the purine salvage pathway, which converts exogenous purines (bases or nucleosides) to nucleotides in Escherichia coli[1].
StructureStructure
XGPRT is a tetramer and contains in each subunit. The ligands are boric acid, magnesium ion, PCP, and Xanthine. Magnesium ions are bound at the active site[2]. The subunits are arranged so three of the four subunits contribute residues to each of the four active sites in the tetramer, and this arrangement observed for XGPRT explains why tetramers are required for enzyme function[1]. XGPRT has a conserved sequence,85-IVIDDLVDTG-94, which is called the PRib-PP (5-phospho-a-D-ribosyl-1-pyrophosphate) (The binding sites of each subunit is shown in pink). This binding site features two adjacent acidic residues, which are surrounded by hydrophobic residues[1]. There is a five-stranded b-sheet surrounded by three or four a-helices that creates a conserved structural core containing the PRib-PP binding site[1]. Another region of the sequence in XGTPase forms a loop, which is involved in substrate recognition[1]. A C-terminal tail is incorporated in the structure of XGPRT and none of the other PRTase structures [1]. The tail from each subunit interacts with residues from the other subunits in tetramer [1].
Mechanism and CatalysisMechanism and Catalysis
|
The reaction catalyzed by XGPRT uses PRib-PP and a nitrogenous base to liberate a pyrophosphate and form a nucleoside monophosphate [1]. The purine base selectivity is achieved by side-chain interactions [1]. Magnesium and other divalent cations are necessary for catalysis because magnesium and PRib-PP binding play a critical role for the PRTase reaction[1]. The Mg:PRib-PP complex binds to the active site of PRTases[1]. XGPRT catalysis proceeds via SN1 mechanism and it forms a oxocarbonium ion in the transition state[1]. It has been suggested, that the magnesium ion departs with the displaced pyrophosphate because there is no magnesium ion at the active site, this has been determined by looking at crystal structures[1].
In the (shown in red) of the XGPRT, there are several residues that are critical for substrate and catalysis[1]. The loop required for binding and catalysis is flexible, when XGPRT does not have products or substrates bound to it[1]. The flexibility of the residues in this loop assists movement of the loop towards the active site[1]. An additional role of the mobile loop is to cover the active site during catalysis to prevent water molecules from capturing the transition state intermediate [1].
Additional ResourcesAdditional Resources
For additional information on PRTases, see: Sandbox Reserved 317
ReferencesReferences
- ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 1.14 1.15 1.16 1.17 1.18 1.19 Vos S, Parry RJ, Burns MR, de Jersey J, Martin JL. Structures of free and complexed forms of Escherichia coli xanthine-guanine phosphoribosyltransferase. J Mol Biol. 1998 Oct 2;282(4):875-89. PMID:9743633 doi:10.1006/jmbi.1998.2051
- ↑ Shi W, Li CM, Tyler PC, Furneaux RH, Grubmeyer C, Schramm VL, Almo SC. The 2.0 A structure of human hypoxanthine-guanine phosphoribosyltransferase in complex with a transition-state analog inhibitor. Nat Struct Biol. 1999 Jun;6(6):588-93. PMID:10360366 doi:http://dx.doi.org/10.1038/9376