1g2o: Difference between revisions

Revision as of 13:45, 21 February 2008

CRYSTAL STRUCTURE OF PURINE NUCLEOSIDE PHOSPHORYLASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH A TRANSITION-STATE INHIBITOR

OverviewOverview

A structural genomics comparison of purine nucleoside phosphorylases (PNPs) indicated that the enzyme encoded by Mycobacterium tuberculosis (TB-PNP) resembles the mammalian trimeric structure rather than the bacterial hexameric PNPs. The crystal structure of M. tuberculosis PNP in complex with the transition-state analogue immucillin-H (ImmH) and inorganic phosphate was solved at 1.75 A resolution and confirms the trimeric structure. Binding of the inhibitor occurs independently at the three catalytic sites, unlike mammalian PNPs which demonstrate negative cooperativity in ImmH binding. Reduced subunit interface contacts for TB-PNP, compared to the mammalian enzymes, correlate with the loss of the cooperative inhibitor binding. Mammalian and TB-PNPs both exhibit slow-onset inhibition and picomolar dissociation constants for ImmH. The structure supports a catalytic mechanism of reactant destabilization by neighboring group electrostatic interactions, transition-state stabilization, and leaving group activation. Despite an overall amino acid sequence identity of 33% between bovine and TB-PNPs and almost complete conservation in active site residues, one catalytic site difference suggests a strategy for the design of transition-state analogues with specificity for TB-PNP. The structure of TB-PNP was also solved to 2.0 A with 9-deazahypoxanthine (9dHX), iminoribitol (IR), and PO(4) to reconstruct the ImmH complex with its separate components. One subunit of the trimer has 9dHX, IR, and PO(4) bound, while the remaining two subunits contain only 9dHX. In the filled subunit, 9dHX retains the contacts found in the ImmH complex. However, the region of IR that corresponds to the oxocarbenium ion is translocated in the direction of the reaction coordinate, and the nucleophilic phosphate rotates away from the IR group. Loose packing of the pieces of ImmH in the catalytic site establishes that covalent connectivity in ImmH is required to achieve the tightly bound complex.

About this StructureAbout this Structure

1G2O is a Single protein structure of sequence from Mycobacterium tuberculosis with and as ligands. Active as Purine-nucleoside phosphorylase, with EC number 2.4.2.1 Full crystallographic information is available from OCA.

ReferenceReference

Structures of purine nucleoside phosphorylase from Mycobacterium tuberculosis in complexes with immucillin-H and its pieces., Shi W, Basso LA, Santos DS, Tyler PC, Furneaux RH, Blanchard JS, Almo SC, Schramm VL, Biochemistry. 2001 Jul 27;40(28):8204-15. PMID:11444966

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OCA

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-[[Image:1g2o.gif|left|200px]]<br /><applet load="1g2o" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1g2o.gif|left|200px]]<br /><applet load="1g2o" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1g2o, resolution 1.75&Aring;" />
 '''CRYSTAL STRUCTURE OF PURINE NUCLEOSIDE PHOSPHORYLASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH A TRANSITION-STATE INHIBITOR'''<br />
 ==Overview==
-A structural genomics comparison of purine nucleoside phosphorylases, (PNPs) indicated that the enzyme encoded by Mycobacterium tuberculosis, (TB-PNP) resembles the mammalian trimeric structure rather than the, bacterial hexameric PNPs. The crystal structure of M. tuberculosis PNP in, complex with the transition-state analogue immucillin-H (ImmH) and, inorganic phosphate was solved at 1.75 A resolution and confirms the, trimeric structure. Binding of the inhibitor occurs independently at the, three catalytic sites, unlike mammalian PNPs which demonstrate negative, cooperativity in ImmH binding. Reduced subunit interface contacts for, TB-PNP, compared to the mammalian enzymes, correlate with the loss of the, cooperative inhibitor binding. Mammalian and TB-PNPs both exhibit, slow-onset inhibition and picomolar dissociation constants for ImmH. The, structure supports a catalytic mechanism of reactant destabilization by, neighboring group electrostatic interactions, transition-state, stabilization, and leaving group activation. Despite an overall amino acid, sequence identity of 33% between bovine and TB-PNPs and almost complete, conservation in active site residues, one catalytic site difference, suggests a strategy for the design of transition-state analogues with, specificity for TB-PNP. The structure of TB-PNP was also solved to 2.0 A, with 9-deazahypoxanthine (9dHX), iminoribitol (IR), and PO(4) to, reconstruct the ImmH complex with its separate components. One subunit of, the trimer has 9dHX, IR, and PO(4) bound, while the remaining two subunits, contain only 9dHX. In the filled subunit, 9dHX retains the contacts found, in the ImmH complex. However, the region of IR that corresponds to the, oxocarbenium ion is translocated in the direction of the reaction, coordinate, and the nucleophilic phosphate rotates away from the IR group., Loose packing of the pieces of ImmH in the catalytic site establishes that, covalent connectivity in ImmH is required to achieve the tightly bound, complex.
+A structural genomics comparison of purine nucleoside phosphorylases (PNPs) indicated that the enzyme encoded by Mycobacterium tuberculosis (TB-PNP) resembles the mammalian trimeric structure rather than the bacterial hexameric PNPs. The crystal structure of M. tuberculosis PNP in complex with the transition-state analogue immucillin-H (ImmH) and inorganic phosphate was solved at 1.75 A resolution and confirms the trimeric structure. Binding of the inhibitor occurs independently at the three catalytic sites, unlike mammalian PNPs which demonstrate negative cooperativity in ImmH binding. Reduced subunit interface contacts for TB-PNP, compared to the mammalian enzymes, correlate with the loss of the cooperative inhibitor binding. Mammalian and TB-PNPs both exhibit slow-onset inhibition and picomolar dissociation constants for ImmH. The structure supports a catalytic mechanism of reactant destabilization by neighboring group electrostatic interactions, transition-state stabilization, and leaving group activation. Despite an overall amino acid sequence identity of 33% between bovine and TB-PNPs and almost complete conservation in active site residues, one catalytic site difference suggests a strategy for the design of transition-state analogues with specificity for TB-PNP. The structure of TB-PNP was also solved to 2.0 A with 9-deazahypoxanthine (9dHX), iminoribitol (IR), and PO(4) to reconstruct the ImmH complex with its separate components. One subunit of the trimer has 9dHX, IR, and PO(4) bound, while the remaining two subunits contain only 9dHX. In the filled subunit, 9dHX retains the contacts found in the ImmH complex. However, the region of IR that corresponds to the oxocarbenium ion is translocated in the direction of the reaction coordinate, and the nucleophilic phosphate rotates away from the IR group. Loose packing of the pieces of ImmH in the catalytic site establishes that covalent connectivity in ImmH is required to achieve the tightly bound complex.
 ==About this Structure==
-G2O is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis] with PO4 and IMH as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Purine-nucleoside_phosphorylase Purine-nucleoside phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.1 2.4.2.1] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1G2O OCA].
+G2O is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis] with <scene name='pdbligand=PO4:'>PO4</scene> and <scene name='pdbligand=IMH:'>IMH</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Purine-nucleoside_phosphorylase Purine-nucleoside phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.1 2.4.2.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G2O OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: Purine-nucleoside phosphorylase]]
 [[Category: Single protein]]
-[[Category: Almo, S.C.]]
+[[Category: Almo, S C.]]
-[[Category: Basso, L.A.]]
+[[Category: Basso, L A.]]
-[[Category: Blanchard, J.S.]]
+[[Category: Blanchard, J S.]]
-[[Category: Furneaux, R.H.]]
+[[Category: Furneaux, R H.]]
-[[Category: Schramm, V.L.]]
+[[Category: Schramm, V L.]]
 [[Category: Shi, W.]]
-[[Category: Tyler, P.C.]]
+[[Category: Tyler, P C.]]
 [[Category: IMH]]
 [[Category: PO4]]
@@ Line 26: / Line 26: @@
 [[Category: trimer]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 15:38:58 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:45:23 2008''