Sandbox Reserved 342: Difference between revisions
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XGPRT is an enzyme that catalyzes the conversion of guanine, xanthine, and sometimes hypoxanthine, to GMP, XMP, and IMP <ref name="Vos"/>. This enzyme is part of the purine salvage pathway, which converts exogenous purines (bases or nucleosides) to nucleotides in ''Escherichia coli''<ref name="Vos"/>. | XGPRT is an enzyme that catalyzes the conversion of guanine, xanthine, and sometimes hypoxanthine, to GMP, XMP, and IMP <ref name="Vos"/>. This enzyme is part of the purine salvage pathway, which converts exogenous purines (bases or nucleosides) to nucleotides in ''Escherichia coli''<ref name="Vos"/>. | ||
=Structure= | =Structure= | ||
XGPRT is a tetramer and contains <scene name='Sandbox_Reserved_342/Ligands/1'>ligands</scene> in each subunit. The ligands are boric acid, magnesium ion, PCP, and Xanthine. Magnesium ions are bound at the active site<ref name="Shi"> PMID:10360366 </ref>. 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<ref name="Vos"/>. XGPRT has a conserved sequence,85-IVIDDLVDTG-94, which is called the PRib-PP (5-phospho-a-D-ribosyl-1-pyrophosphate) <scene name='Sandbox_Reserved_342/Prib-pp_binding_site/3'>binding site</scene> (The binding sites of each subunit is shown in pink). This binding site features two adjacent acidic residues, which are surrounded by hydrophobic residues<ref name="Vos"/>. 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<ref name="Vos"/>. | XGPRT is a tetramer and contains <scene name='Sandbox_Reserved_342/Ligands/1'>ligands</scene> in each subunit. The ligands are boric acid, magnesium ion, PCP, and Xanthine. Magnesium ions are bound at the active site<ref name="Shi"> PMID:10360366 </ref>. 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<ref name="Vos"/>. XGPRT has a conserved sequence,85-IVIDDLVDTG-94, which is called the PRib-PP (5-phospho-a-D-ribosyl-1-pyrophosphate) <scene name='Sandbox_Reserved_342/Prib-pp_binding_site/3'>binding site</scene> (The binding sites of each subunit is shown in pink). This binding site features two adjacent acidic residues, which are surrounded by hydrophobic residues<ref name="Vos"/>. 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<ref name="Vos"/>. Another region of the sequence in XGTPase forms a loop, which is involved in substrate recognition<ref name="Vos"/>. A C-terminal tail is incorporated in the structure of XGPRT and none of the other PRTase structures <ref name="Vos"/>. The tail from each subunit interacts with residues from the other subunits in tetramer <ref name="Vos"/>. | ||
=Mechanism and Catalysis= | =Mechanism and Catalysis= | ||
<Structure load='1a96' size='300' frame='true' align='right' caption='Xanthine-guanine Phosphoribosyltransferase' scene='Insert optional scene name here' /> | <Structure load='1a96' size='300' frame='true' align='right' caption='Xanthine-guanine Phosphoribosyltransferase' scene='Insert optional scene name here' /> | ||
The reaction catalyzed by XGPRT uses PRib-PP and a nitrogenous base to liberate a pyrophosphate and form a nucleoside monophosphate <ref name="Vos"/>. Magnesium and other divalent cations are necessary for catalysis because magnesium and PRib-PP binding play a critical role for the PRTase reaction<ref name="Vos"/>. The Mg:PRib-PP complex binds to the active site of PRTases<ref name="Vos"/>. XGPRT catalysis proceeds via SN1 mechanism and it forms a oxocarbonium ion in the transition state<ref name="Vos"/>. 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<ref name="Vos"/>. | The reaction catalyzed by XGPRT uses PRib-PP and a nitrogenous base to liberate a pyrophosphate and form a nucleoside monophosphate <ref name="Vos"/>. The purine base selectivity is achieved by side-chain interactions <ref name="Vos"/>. Magnesium and other divalent cations are necessary for catalysis because magnesium and PRib-PP binding play a critical role for the PRTase reaction<ref name="Vos"/>. The Mg:PRib-PP complex binds to the active site of PRTases<ref name="Vos"/>. XGPRT catalysis proceeds via SN1 mechanism and it forms a oxocarbonium ion in the transition state<ref name="Vos"/>. 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<ref name="Vos"/>. | ||
In the <scene name='Sandbox_Reserved_342/Mobile_loop/1'>mobile loop</scene> (shown in red) of the XGPRT, there are several residues that are critical for substrate and catalysis<ref name="Vos"/>. The loop required for binding and catalysis is flexible, when XGPRT does not have products or substrates bound to it<ref name="Vos"/>. The flexibility of the residues in this loop assists movement of the loop towards the active site<ref name="Vos"/>. 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 <ref name="Vos"/>. | In the <scene name='Sandbox_Reserved_342/Mobile_loop/1'>mobile loop</scene> (shown in red) of the XGPRT, there are several residues that are critical for substrate and catalysis<ref name="Vos"/>. The loop required for binding and catalysis is flexible, when XGPRT does not have products or substrates bound to it<ref name="Vos"/>. The flexibility of the residues in this loop assists movement of the loop towards the active site<ref name="Vos"/>. 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 <ref name="Vos"/>. | ||
=Additional Resources= | =Additional Resources= | ||