1b8n: Difference between revisions

Revision as of 12:52, 21 February 2008

PURINE NUCLEOSIDE PHOSPHORYLASE

OverviewOverview

Immucillin-H (ImmH) and immucillin-G (ImmG) were previously reported as transition-state analogues for bovine purine nucleoside phosphorylase (PNP) and are the most powerful inhibitors reported for the enzyme (K(i) = 23 and 30 pM). Sixteen new immucillins are used to probe the atomic interactions that cause tight binding for bovine PNP. Eight analogues of ImmH are identified with equilibrium dissociation constants of 1 nM or below. A novel crystal structure of bovine PNP-ImmG-PO(4) is described. Crystal structures of ImmH and ImmG bound to bovine PNP indicate that nearly every H-bond donor/acceptor site on the inhibitor is fully engaged in favorable H-bond partners. Chemical modification of the immucillins is used to quantitate the energetics for each contact at the catalytic site. Conversion of the 6-carbonyl oxygen to a 6-amino group (ImmH to ImmA) increases the dissociation constant from 23 pM to 2.6 million pM. Conversion of the 4'-imino group to a 4'-oxygen (ImmH to 9-deazainosine) increases the dissociation constant from 23 pM to 2.0 million pM. Substituents that induce small pK(a) changes at N-7 demonstrate modest loss of affinity. Thus, 8-F or 8-CH(3)-substitutions decrease affinity less than 10-fold. But a change in the deazapurine ring to convert N-7 from a H-bond donor to a H-bond acceptor (ImmH to 4-aza-3-deaza-ImmH) decreases affinity by >10(7). Introduction of a methylene bridge between 9-deazahypoxanthine and the iminoribitol (9-(1'-CH(2))-ImmH) increased the distance between leaving and oxacarbenium groups and increased K(i) to 91 000 pM. Catalytic site energetics for 20 substitutions in the transition-state analogue are analyzed in this approach. Disruption of the H-bond pattern that defines the transition-state ensemble leads to a large decrease in binding affinity. Changes in a single H-bond contact site cause up to 10.1 kcal/mol loss of binding energy, requiring a cooperative H-bond pattern in binding the transition-state analogues. Groups involved in leaving group activation and ribooxacarbenium ion stabilization are central to the H-bond network that provides transition-state stabilization and tight binding of the immucillins.

About this StructureAbout this Structure

1B8N is a Single protein structure of sequence from Bos taurus with , and as ligands. Active as Purine-nucleoside phosphorylase, with EC number 2.4.2.1 Full crystallographic information is available from OCA.

ReferenceReference

Atomic dissection of the hydrogen bond network for transition-state analogue binding to purine nucleoside phosphorylase., Kicska GA, Tyler PC, Evans GB, Furneaux RH, Shi W, Fedorov A, Lewandowicz A, Cahill SM, Almo SC, Schramm VL, Biochemistry. 2002 Dec 10;41(49):14489-98. PMID:12463747

Page seeded by OCA on Thu Feb 21 11:52:39 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

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-[[Image:1b8n.gif|left|200px]]<br /><applet load="1b8n" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1b8n.gif|left|200px]]<br /><applet load="1b8n" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1b8n, resolution 2.00&Aring;" />
 '''PURINE NUCLEOSIDE PHOSPHORYLASE'''<br />
 ==Overview==
-Immucillin-H (ImmH) and immucillin-G (ImmG) were previously reported as, transition-state analogues for bovine purine nucleoside phosphorylase, (PNP) and are the most powerful inhibitors reported for the enzyme (K(i) =, 23 and 30 pM). Sixteen new immucillins are used to probe the atomic, interactions that cause tight binding for bovine PNP. Eight analogues of, ImmH are identified with equilibrium dissociation constants of 1 nM or, below. A novel crystal structure of bovine PNP-ImmG-PO(4) is described., Crystal structures of ImmH and ImmG bound to bovine PNP indicate that, nearly every H-bond donor/acceptor site on the inhibitor is fully engaged, in favorable H-bond partners. Chemical modification of the immucillins is, used to quantitate the energetics for each contact at the catalytic site., Conversion of the 6-carbonyl oxygen to a 6-amino group (ImmH to ImmA), increases the dissociation constant from 23 pM to 2.6 million pM., Conversion of the 4'-imino group to a 4'-oxygen (ImmH to 9-deazainosine), increases the dissociation constant from 23 pM to 2.0 million pM., Substituents that induce small pK(a) changes at N-7 demonstrate modest, loss of affinity. Thus, 8-F or 8-CH(3)-substitutions decrease affinity, less than 10-fold. But a change in the deazapurine ring to convert N-7, from a H-bond donor to a H-bond acceptor (ImmH to 4-aza-3-deaza-ImmH), decreases affinity by &gt;10(7). Introduction of a methylene bridge between, 9-deazahypoxanthine and the iminoribitol (9-(1'-CH(2))-ImmH) increased the, distance between leaving and oxacarbenium groups and increased K(i) to 91, 000 pM. Catalytic site energetics for 20 substitutions in the, transition-state analogue are analyzed in this approach. Disruption of the, H-bond pattern that defines the transition-state ensemble leads to a large, decrease in binding affinity. Changes in a single H-bond contact site, cause up to 10.1 kcal/mol loss of binding energy, requiring a cooperative, H-bond pattern in binding the transition-state analogues. Groups involved, in leaving group activation and ribooxacarbenium ion stabilization are, central to the H-bond network that provides transition-state stabilization, and tight binding of the immucillins.
+Immucillin-H (ImmH) and immucillin-G (ImmG) were previously reported as transition-state analogues for bovine purine nucleoside phosphorylase (PNP) and are the most powerful inhibitors reported for the enzyme (K(i) = 23 and 30 pM). Sixteen new immucillins are used to probe the atomic interactions that cause tight binding for bovine PNP. Eight analogues of ImmH are identified with equilibrium dissociation constants of 1 nM or below. A novel crystal structure of bovine PNP-ImmG-PO(4) is described. Crystal structures of ImmH and ImmG bound to bovine PNP indicate that nearly every H-bond donor/acceptor site on the inhibitor is fully engaged in favorable H-bond partners. Chemical modification of the immucillins is used to quantitate the energetics for each contact at the catalytic site. Conversion of the 6-carbonyl oxygen to a 6-amino group (ImmH to ImmA) increases the dissociation constant from 23 pM to 2.6 million pM. Conversion of the 4'-imino group to a 4'-oxygen (ImmH to 9-deazainosine) increases the dissociation constant from 23 pM to 2.0 million pM. Substituents that induce small pK(a) changes at N-7 demonstrate modest loss of affinity. Thus, 8-F or 8-CH(3)-substitutions decrease affinity less than 10-fold. But a change in the deazapurine ring to convert N-7 from a H-bond donor to a H-bond acceptor (ImmH to 4-aza-3-deaza-ImmH) decreases affinity by &gt;10(7). Introduction of a methylene bridge between 9-deazahypoxanthine and the iminoribitol (9-(1'-CH(2))-ImmH) increased the distance between leaving and oxacarbenium groups and increased K(i) to 91 000 pM. Catalytic site energetics for 20 substitutions in the transition-state analogue are analyzed in this approach. Disruption of the H-bond pattern that defines the transition-state ensemble leads to a large decrease in binding affinity. Changes in a single H-bond contact site cause up to 10.1 kcal/mol loss of binding energy, requiring a cooperative H-bond pattern in binding the transition-state analogues. Groups involved in leaving group activation and ribooxacarbenium ion stabilization are central to the H-bond network that provides transition-state stabilization and tight binding of the immucillins.
 ==About this Structure==
-B8N is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] with MG, PO4 and IMG 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=1B8N OCA].
+B8N is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] with <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=PO4:'>PO4</scene> and <scene name='pdbligand=IMG:'>IMG</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=1B8N OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: Purine-nucleoside phosphorylase]]
 [[Category: Single protein]]
-[[Category: Almo, S.C.]]
+[[Category: Almo, S C.]]
-[[Category: Fedorov, A.A.]]
+[[Category: Fedorov, A A.]]
-[[Category: Fedorov, E.V.]]
+[[Category: Fedorov, E V.]]
-[[Category: Furneaux, R.H.]]
+[[Category: Furneaux, R H.]]
-[[Category: Kicska, G.A.]]
+[[Category: Kicska, G A.]]
-[[Category: Schramm, V.L.]]
+[[Category: Schramm, V L.]]
-[[Category: Strokopytov, B.V.]]
+[[Category: Strokopytov, B V.]]
-[[Category: Tyler, P.C.]]
+[[Category: Tyler, P C.]]
 [[Category: IMG]]
 [[Category: MG]]
@@ Line 28: / Line 28: @@
 [[Category: purine nucleoside phosphorylase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 11:27:22 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:52:39 2008''