This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


2isc

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:04, 21 February 2024) (edit) (undo)
 
(13 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2isc.jpg|left|200px]]
 
-
<!--
+
==Crystal structure of Purine Nucleoside Phosphorylase from Trichomonas vaginalis with DADMe-Imm-A==
-
The line below this paragraph, containing "STRUCTURE_2isc", creates the "Structure Box" on the page.
+
<StructureSection load='2isc' size='340' side='right'caption='[[2isc]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[2isc]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Trichomonas_vaginalis Trichomonas vaginalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ISC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ISC FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=223:(3R,4R)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-4-(HYDROXYMETHYL)PYRROLIDIN-3-OL'>223</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-
{{STRUCTURE_2isc| PDB=2isc | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2isc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2isc OCA], [https://pdbe.org/2isc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2isc RCSB], [https://www.ebi.ac.uk/pdbsum/2isc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2isc ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/A2E7Y6_TRIV3 A2E7Y6_TRIV3]
 +
== 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/is/2isc_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2isc ConSurf].
 +
<div style="clear:both"></div>
-
'''Crystal stucture of Purine Nucleoside Phosphorylase from Trichomonas vaginalis with DADMe-Imm-A'''
+
==See Also==
-
 
+
*[[Purine nucleoside phosphorylase 3D structures|Purine nucleoside phosphorylase 3D structures]]
-
 
+
__TOC__
-
==Overview==
+
</StructureSection>
-
Trichomonas vaginalis is a parasitic protozoan purine auxotroph possessing a unique purine salvage pathway consisting of a bacterial type purine nucleoside phosphorylase (PNP) and a purine nucleoside kinase. Thus, T. vaginalis PNP (TvPNP) functions in the reverse direction relative to the PNPs in other organisms. Immucillin-A (ImmA) and DADMe-Immucillin-A (DADMe-ImmA) are transition state mimics of adenosine with geometric and electrostatic features that resemble early and late transition states of adenosine at the transition state stabilized by TvPNP. ImmA demonstrates slow-onset tight-binding inhibition with TvPNP, to give an equilibrium dissociation constant of 87 pM, an inhibitor release half-time of 17.2 min, and a Km/Kd ratio of 70,100. DADMe-ImmA resembles a late ribooxacarbenium ion transition state for TvPNP to give a dissociation constant of 30 pM, an inhibitor release half-time of 64 min, and a Km/Kd ratio of 203,300. The tight binding of DADMe-ImmA supports a late SN1 transition state. Despite their tight binding to TvPNP, ImmA and DADMe-ImmA are weak inhibitors of human and P. falciparum PNPs. The crystal structures of the TvPNP x ImmA x PO4 and TvPNP x DADMe-ImmA x PO4 ternary complexes differ from previous structures with substrate analogues. The tight binding with DADMe-ImmA is in part due to a 2.7 A ionic interaction between a PO4 oxygen and the N1' cation of the hydroxypyrrolidine and is weaker in the TvPNP x ImmA x PO4 structure at 3.5 A. However, the TvPNP x ImmA x PO4 structure includes hydrogen bonds between the 2'-hydroxyl and the protein that are not present in TvPNP x DADMe-ImmA x PO4. These structures explain why DADMe-ImmA binds tighter than ImmA. Immucillin-H is a 12 nM inhibitor of TvPNP but a 56 pM inhibitor of human PNP. And this difference is explained by isotope-edited difference infrared spectroscopy with [6-18O]ImmH to establish that O6 is the keto tautomer in TvPNP x ImmH x PO4, causing an unfavorable leaving-group interaction.
+
[[Category: Large Structures]]
-
 
+
[[Category: Trichomonas vaginalis]]
-
==About this Structure==
+
[[Category: Almo SC]]
-
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ISC OCA].
+
[[Category: Rinaldo-Matthis A]]
-
 
+
[[Category: Schramm VL]]
-
==Reference==
+
-
Inhibition and structure of Trichomonas vaginalis purine nucleoside phosphorylase with picomolar transition state analogues., Rinaldo-Matthis A, Wing C, Ghanem M, Deng H, Wu P, Gupta A, Tyler PC, Evans GB, Furneaux RH, Almo SC, Wang CC, Schramm VL, Biochemistry. 2007 Jan 23;46(3):659-68. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17223688 17223688]
+
-
[[Category: Purine-nucleoside phosphorylase]]
+
-
[[Category: Almo, S C.]]
+
-
[[Category: Rinaldo-Matthis, A.]]
+
-
[[Category: Schramm, V L.]]
+
-
[[Category: Purine nucleoside phosphorylase]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 07:48:32 2008''
+

Current revision

Crystal structure of Purine Nucleoside Phosphorylase from Trichomonas vaginalis with DADMe-Imm-A

PDB ID 2isc

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2isc"
Personal tools