2p4s

From Proteopedia

(Difference between revisions)

Current revision

Structure of Purine Nucleoside Phosphorylase from Anopheles gambiae in complex with DADMe-ImmH

Structural highlights

2p4s is a 3 chain structure with sequence from Anopheles gambiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.2Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PNPH_ANOGA As part of the purine salvage pathway, catalyzes the phosphorolytic breakdown of the N-glycosidic bond in the beta-(deoxy)ribonucleoside molecules, with the formation of the corresponding free purine bases and pentose-1-phosphate (PubMed:17918964). Preferentially acts on 2'-deoxyinosine and inosine, and to a lesser extent on 2'-deoxyguanosine and guanosine (PubMed:17918964). Has no activity towards adenosine or 2'-deoxyadenosine (PubMed:17918964).^[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The purine salvage pathway of Anopheles gambiae, a mosquito that transmits malaria, has been identified in genome searches on the basis of sequence homology with characterized enzymes. Purine nucleoside phosphorylase (PNP) is a target for the development of therapeutic agents in humans and purine auxotrophs, including malarial parasites. The PNP from Anopheles gambiae (AgPNP) was expressed in Escherichia coli and compared to the PNPs from Homo sapiens (HsPNP) and Plasmodium falciparum (PfPNP). AgPNP has kcat values of 54 and 41 s-1 for 2'-deoxyinosine and inosine, its preferred substrates, and 1.0 s-1 for guanosine. However, the chemical step is fast for AgPNP at 226 s-1 for guanosine in pre-steady-state studies. 5'-Deaza-1'-aza-2'-deoxy-1'-(9-methylene)-Immucillin-H (DADMe-ImmH) is a transition-state mimic for a 2'-deoxyinosine ribocation with a fully dissociated N-ribosidic bond and is a slow-onset, tight-binding inhibitor with a dissociation constant of 3.5 pM. This is the tightest-binding inhibitor known for any PNP, with a remarkable Km/Ki* of 5.4 x 10(7), and is consistent with enzymatic transition state predictions of enhanced transition-state analogue binding in enzymes with enhanced catalytic efficiency. Deoxyguanosine is a weaker substrate than deoxyinosine, and DADMe-Immucillin-G is less tightly bound than DADMe-ImmH, with a dissociation constant of 23 pM for AgPNP as compared to 7 pM for HsPNP. The crystal structure of AgPNP was determined in complex with DADMe-ImmH and phosphate to a resolution of 2.2 A to reveal the differences in substrate and inhibitor specificity. The distance from the N1' cation to the phosphate O4 anion is shorter in the AgPNP.DADMe-ImmH.PO4 complex than in HsPNP.DADMe-ImmH.SO4, offering one explanation for the stronger inhibitory effect of DADMe-ImmH for AgPNP.

Anopheles gambiae purine nucleoside phosphorylase: catalysis, structure, and inhibition.,Taylor EA, Rinaldo-Matthis A, Li L, Ghanem M, Hazleton KZ, Cassera MB, Almo SC, Schramm VL Biochemistry. 2007 Oct 30;46(43):12405-15. Epub 2007 Oct 6. PMID:17918964^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Taylor EA, Rinaldo-Matthis A, Li L, Ghanem M, Hazleton KZ, Cassera MB, Almo SC, Schramm VL. Anopheles gambiae purine nucleoside phosphorylase: catalysis, structure, and inhibition. Biochemistry. 2007 Oct 30;46(43):12405-15. Epub 2007 Oct 6. PMID:17918964 doi:10.1021/bi7010256
↑ Taylor EA, Rinaldo-Matthis A, Li L, Ghanem M, Hazleton KZ, Cassera MB, Almo SC, Schramm VL. Anopheles gambiae purine nucleoside phosphorylase: catalysis, structure, and inhibition. Biochemistry. 2007 Oct 30;46(43):12405-15. Epub 2007 Oct 6. PMID:17918964 doi:10.1021/bi7010256

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2p4s"

Categories: Anopheles gambiae | Large Structures | Almo SC | Rinaldo-Matthis A | Schramm VL

@@ Line 1: / Line 1: @@
 ==Structure of Purine Nucleoside Phosphorylase from Anopheles gambiae in complex with DADMe-ImmH==
-<StructureSection load='2p4s' size='340' side='right' caption='[[2p4s]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+<StructureSection load='2p4s' size='340' side='right'caption='[[2p4s]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2p4s]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Anoga Anoga]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2P4S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2P4S FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2p4s]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Anopheles_gambiae Anopheles gambiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2P4S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2P4S FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DIH:3-HYDROXY-4-HYDROXYMETHYL-1-(4-OXO-4,4A,5,7A-TETRAHYDRO-3H-PYRROLO[3,2-D]PYRIMIDIN-7-YLMETHYL)-PYRROLIDINIUM'>DIH</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pnp ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7165 ANOGA])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DIH:3-HYDROXY-4-HYDROXYMETHYL-1-(4-OXO-4,4A,5,7A-TETRAHYDRO-3H-PYRROLO[3,2-D]PYRIMIDIN-7-YLMETHYL)-PYRROLIDINIUM'>DIH</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2p4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p4s OCA], [https://pdbe.org/2p4s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2p4s RCSB], [https://www.ebi.ac.uk/pdbsum/2p4s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2p4s ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2p4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p4s OCA], [http://pdbe.org/2p4s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2p4s RCSB], [http://www.ebi.ac.uk/pdbsum/2p4s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2p4s ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/PNPH_ANOGA PNPH_ANOGA] As part of the purine salvage pathway, catalyzes the phosphorolytic breakdown of the N-glycosidic bond in the beta-(deoxy)ribonucleoside molecules, with the formation of the corresponding free purine bases and pentose-1-phosphate (PubMed:17918964). Preferentially acts on 2'-deoxyinosine and inosine, and to a lesser extent on 2'-deoxyguanosine and guanosine (PubMed:17918964). Has no activity towards adenosine or 2'-deoxyadenosine (PubMed:17918964).<ref>PMID:17918964</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/p4/2p4s_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/p4/2p4s_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 28: / Line 29: @@
 </div>
 <div class="pdbe-citations 2p4s" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Purine nucleoside phosphorylase 3D structures|Purine nucleoside phosphorylase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Anoga]]
+[[Category: Anopheles gambiae]]
-[[Category: Purine-nucleoside phosphorylase]]
+[[Category: Large Structures]]
-[[Category: Almo, S C]]
+[[Category: Almo SC]]
-[[Category: Rinaldo-Matthis, A]]
+[[Category: Rinaldo-Matthis A]]
-[[Category: Schramm, V L]]
+[[Category: Schramm VL]]
-[[Category: Purine nucleoside phosphorylase]]
-[[Category: Transferase]]

2p4s

From Proteopedia

Current revision

Structure of Purine Nucleoside Phosphorylase from Anopheles gambiae in complex with DADMe-ImmH

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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