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.


1dqp

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:57, 7 February 2024) (edit) (undo)
 
(13 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1dqp.jpg|left|200px]]
 
-
{{Structure
+
==CRYSTAL STRUCTURE OF GIARDIA GUANINE PHOSPHORIBOSYLTRANSFERASE COMPLEXED WITH IMMUCILLING==
-
|PDB= 1dqp |SIZE=350|CAPTION= <scene name='initialview01'>1dqp</scene>, resolution 1.75&Aring;
+
<StructureSection load='1dqp' size='340' side='right'caption='[[1dqp]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=IMG:1,4-DIDEOXY-1,4-IMINO-1-(S)-(9-DEAZAGUANIN-9-YL)-D-RIBITOL'>IMG</scene> and <scene name='pdbligand=IPA:ISOPROPYL ALCOHOL'>IPA</scene>
+
<table><tr><td colspan='2'>[[1dqp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Giardia_intestinalis Giardia intestinalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DQP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DQP FirstGlance]. <br>
-
|ACTIVITY= [http://en.wikipedia.org/wiki/Hypoxanthine_phosphoribosyltransferase Hypoxanthine phosphoribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.8 2.4.2.8]
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.75&#8491;</td></tr>
-
|GENE=
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IMG:1,4-DIDEOXY-1,4-IMINO-1-(S)-(9-DEAZAGUANIN-9-YL)-D-RIBITOL'>IMG</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene></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=1dqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dqp OCA], [https://pdbe.org/1dqp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dqp RCSB], [https://www.ebi.ac.uk/pdbsum/1dqp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dqp ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/Q24973_GIAIN Q24973_GIAIN]
 +
== 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/dq/1dqp_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=1dqp ConSurf].
 +
<div style="clear:both"></div>
-
'''CRYSTAL STRUCTURE OF GIARDIA GUANINE PHOSPHORIBOSYLTRANSFERASE COMPLEXED WITH IMMUCILLING'''
+
==See Also==
-
 
+
*[[Phosphoribosyltransferase 3D structures|Phosphoribosyltransferase 3D structures]]
-
 
+
__TOC__
-
==Overview==
+
</StructureSection>
-
Giardia lamblia, the protozoan parasite responsible for giardiasis, requires purine salvage from its host for RNA and DNA synthesis. G. lamblia expresses an unusual purine phosphoribosyltransferase with a high specificity for guanine (GPRTase). The enzyme's sequence significantly diverges from those of related enzymes in other organisms. The transition state analogue immucillinGP is a powerful inhibitor of HGXPRTase from malaria [Li, C. M., et al. (1999) Nat. Struct. Biol. 6, 582-587] and is also a 10 nM inhibitor of G. lamblia GPRTase. Cocrystallization of GPRTase with immucillinGP led unexpectedly to a GPRTase.immucillinG binary complex with an open catalytic site loop. Diffusion of ligands into preformed crystals gave a GPRTase.immucillinGP.Mg(2+).pyrophosphate complex in which the open loop is stabilized by crystal contacts. G. lamblia GPRTase exhibits substantial structural differences from known purine phosphoribosyltransferases at positions remote from the catalytic site, but conserves most contacts to the bound inhibitor. The filled catalytic site with an open catalytic loop provides insight into ligand binding. One active site Mg(2+) ion is chelated to pyrophosphate, but the other is chelated to two conserved catalytic site carboxylates, suggesting a role for these amino acids. This arrangement of Mg(2+) and pyrophosphate has not been reported in purine phosphoribosyltransferases. ImmucillinG in the binary complex is anchored by its 9-deazaguanine group, and the iminoribitol is disordered. No Mg(2+) or pyrophosphate is detected; thus, the 5'-phosphoryl group is needed to immobilize the iminoribitol prior to magnesium pyrophosphate binding. Filling the catalytic site involves (1) binding the purine ring, (2) anchoring the 5'-phosphate to fix the ribosyl group, (3) binding the first Mg(2+) to Asp125 and Glu126 carboxyl groups and binding Mg(2+).pyrophosphate, and (4) closing the catalytic site loop and formation of bound (Mg(2+))(2). pyrophosphate prior to catalysis. Guanine specificity is provided by two peptide carbonyl oxygens hydrogen-bonded to the exocyclic amino group and a weak interaction to O6. Transition state formation involves N7 protonation by Asp129 acting as the general acid.
+
-
 
+
-
==About this Structure==
+
-
1DQP is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Giardia_intestinalis Giardia intestinalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DQP OCA].
+
-
 
+
-
==Reference==
+
-
Crystal structures of Giardia lamblia guanine phosphoribosyltransferase at 1.75 A(,)., Shi W, Munagala NR, Wang CC, Li CM, Tyler PC, Furneaux RH, Grubmeyer C, Schramm VL, Almo SC, Biochemistry. 2000 Jun 13;39(23):6781-90. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10841757 10841757]
+
[[Category: Giardia intestinalis]]
[[Category: Giardia intestinalis]]
-
[[Category: Hypoxanthine phosphoribosyltransferase]]
+
[[Category: Large Structures]]
-
[[Category: Single protein]]
+
[[Category: Almo SC]]
-
[[Category: Almo, S C.]]
+
[[Category: Furneaux RH]]
-
[[Category: Furneaux, R H.]]
+
[[Category: Grubmeyer C]]
-
[[Category: Grubmeyer, C.]]
+
[[Category: Li CM]]
-
[[Category: Li, C M.]]
+
[[Category: Munagala NR]]
-
[[Category: Munagala, N R.]]
+
[[Category: Schramm VL]]
-
[[Category: Schramm, V L.]]
+
[[Category: Shi W]]
-
[[Category: Shi, W.]]
+
[[Category: Tyler PC]]
-
[[Category: Tyler, P C.]]
+
[[Category: Wang CC]]
-
[[Category: Wang, C C.]]
+
-
[[Category: IMG]]
+
-
[[Category: IPA]]
+
-
[[Category: 9-deazaguanine]]
+
-
[[Category: immucilling]]
+
-
[[Category: protein-inhibitor complex]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:42:47 2008''
+

Current revision

CRYSTAL STRUCTURE OF GIARDIA GUANINE PHOSPHORIBOSYLTRANSFERASE COMPLEXED WITH IMMUCILLING

PDB ID 1dqp

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/1dqp"
Personal tools