1bd4: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(12 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1bd4.gif|left|200px]]


{{Structure
==UPRT-URACIL COMPLEX==
|PDB= 1bd4 |SIZE=350|CAPTION= <scene name='initialview01'>1bd4</scene>, resolution 2.2&Aring;
<StructureSection load='1bd4' size='340' side='right'caption='[[1bd4]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=URA:URACIL'>URA</scene>
<table><tr><td colspan='2'>[[1bd4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Toxoplasma_gondii Toxoplasma gondii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BD4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BD4 FirstGlance]. <br>
|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Uracil_phosphoribosyltransferase Uracil phosphoribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.9 2.4.2.9] </span>
</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>
|GENE=
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=URA:URACIL'>URA</scene></td></tr>
|DOMAIN=
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1bd4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bd4 OCA], [https://pdbe.org/1bd4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bd4 RCSB], [https://www.ebi.ac.uk/pdbsum/1bd4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bd4 ProSAT]</span></td></tr>
|RELATEDENTRY=
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1bd4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bd4 OCA], [http://www.ebi.ac.uk/pdbsum/1bd4 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1bd4 RCSB]</span>
== Function ==
}}
[https://www.uniprot.org/uniprot/UPP_TOXGO UPP_TOXGO] Catalyzes the conversion of uracil and 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) to UMP and diphosphate.<ref>PMID:9247925</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/bd/1bd4_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=1bd4 ConSurf].
<div style="clear:both"></div>


'''UPRT-URACIL COMPLEX'''
==See Also==
 
*[[Phosphoribosyltransferase 3D structures|Phosphoribosyltransferase 3D structures]]
 
== References ==
==Overview==
<references/>
Uracil phosphoribosyltransferase (UPRTase) catalyzes the transfer of a ribosyl phosphate group from alpha-D-5-phosphoribosyl-1-pyrophosphate to the N1 nitrogen of uracil. The UPRTase from the opportunistic pathogen Toxoplasma gondii is a rational target for antiparasitic drug design. To aid in structure-based drug design studies against toxoplasmosis, the crystal structures of the T.gondii apo UPRTase (1.93 A resolution), the UPRTase bound to its substrate, uracil (2.2 A resolution), its product, UMP (2.5 A resolution), and the prodrug, 5-fluorouracil (2.3 A resolution), have been determined. These structures reveal that UPRTase recognizes uracil through polypeptide backbone hydrogen bonds to the uracil exocyclic O2 and endocyclic N3 atoms and a backbone-water-exocyclic O4 oxygen hydrogen bond. This stereochemical arrangement and the architecture of the uracil-binding pocket reveal why cytosine and pyrimidines with exocyclic substituents at ring position 5 larger than fluorine, including thymine, cannot bind to the enzyme. Strikingly, the T. gondii UPRTase contains a 22 residue insertion within the conserved PRTase fold that forms an extended antiparallel beta-arm. Leu92, at the tip of this arm, functions to cap the active site of its dimer mate, thereby inhibiting the escape of the substrate-binding water molecule.
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
1BD4 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Toxoplasma_gondii Toxoplasma gondii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BD4 OCA].
 
==Reference==
Crystal structures of Toxoplasma gondii uracil phosphoribosyltransferase reveal the atomic basis of pyrimidine discrimination and prodrug binding., Schumacher MA, Carter D, Scott DM, Roos DS, Ullman B, Brennan RG, EMBO J. 1998 Jun 15;17(12):3219-32. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9628859 9628859]
[[Category: Single protein]]
[[Category: Toxoplasma gondii]]
[[Category: Toxoplasma gondii]]
[[Category: Uracil phosphoribosyltransferase]]
[[Category: Brennan RG]]
[[Category: Brennan, R G.]]
[[Category: Carter D]]
[[Category: Carter, D.]]
[[Category: Roos D]]
[[Category: Roos, D.]]
[[Category: Schumacher MA]]
[[Category: Schumacher, M A.]]
[[Category: Scott D]]
[[Category: Scott, D.]]
[[Category: Ullman B]]
[[Category: Ullman, B.]]
[[Category: complex]]
[[Category: glycosyltransferase]]
[[Category: transferase]]
[[Category: uprt]]
[[Category: uracil]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 18:58:29 2008''

Latest revision as of 09:35, 7 February 2024

UPRT-URACIL COMPLEXUPRT-URACIL COMPLEX

Structural highlights

1bd4 is a 4 chain structure with sequence from Toxoplasma gondii. 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

UPP_TOXGO Catalyzes the conversion of uracil and 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) to UMP and diphosphate.[1]

Evolutionary Conservation

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

See Also

References

  1. ↑ Carter D, Donald RG, Roos D, Ullman B. Expression, purification, and characterization of uracil phosphoribosyltransferase from Toxoplasma gondii. Mol Biochem Parasitol. 1997 Aug;87(2):137-44. PMID:9247925

1bd4, resolution 2.20Å

Drag the structure with the mouse to rotate

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

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=1bd4&oldid=4040511"