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.


1r2r

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:20, 14 February 2024) (edit) (undo)
 
(15 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1r2r.gif|left|200px]]
 
-
{{Structure
+
==CRYSTAL STRUCTURE OF RABBIT MUSCLE TRIOSEPHOSPHATE ISOMERASE==
-
|PDB= 1r2r |SIZE=350|CAPTION= <scene name='initialview01'>1r2r</scene>, resolution 1.50&Aring;
+
<StructureSection load='1r2r' size='340' side='right'caption='[[1r2r]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>
+
<table><tr><td colspan='2'>[[1r2r]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R2R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1R2R FirstGlance]. <br>
-
|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Triose-phosphate_isomerase Triose-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.1 5.3.1.1] </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]] 1.5&#8491;</td></tr>
-
|GENE=
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=1r2r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r2r OCA], [https://pdbe.org/1r2r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1r2r RCSB], [https://www.ebi.ac.uk/pdbsum/1r2r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1r2r ProSAT]</span></td></tr>
-
|RELATEDENTRY=[[1r2s|1R2S]], [[1r2t|1R2T]]
+
</table>
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1r2r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r2r OCA], [http://www.ebi.ac.uk/pdbsum/1r2r PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1r2r RCSB]</span>
+
== Function ==
-
}}
+
[https://www.uniprot.org/uniprot/TPIS_RABIT TPIS_RABIT]
 +
== 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/r2/1r2r_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=1r2r ConSurf].
 +
<div style="clear:both"></div>
-
'''CRYSTAL STRUCTURE OF RABBIT MUSCLE TRIOSEPHOSPHATE ISOMERASE'''
+
==See Also==
-
 
+
*[[Triose phosphate isomerase 3D structures|Triose phosphate isomerase 3D structures]]
-
 
+
__TOC__
-
==Overview==
+
</StructureSection>
-
The active site loop of triosephosphate isomerase (TIM) exhibits a hinged-lid motion, alternating between the two well defined "open" and "closed" conformations. Until now the closed conformation had only been observed in protein complexes with substrate analogues. Here, we present the first rabbit muscle apo TIM structure, refined to 1.5A resolution, in which the active site loop is either in the open or in the closed conformation in different subunits of the enzyme. In the closed conformation described here, the lid loop residues participate in stabilizing hydrogen bonds characteristic of holo TIM structures, whereas chemical interactions observed in the open loop conformation are similar to those found in the apo structures of TIM. In the closed conformation, a number of water molecules are observed at the projected ligand atom positions that are hydrogen bonded to the active site residues. Additives used during crystallization (DMSO and Tris molecules and magnesium atoms) were modeled in the electron density maps. However, no specific binding of these molecules is observed at, or close to, the active site and the lid loop. To further investigate this unusual closed conformation of the apo enzyme, two more rabbit muscle TIM structures, one in the same and another in a different crystal form, were determined. These structures present the open lid conformation only, indicating that the closed conformation cannot be explained by crystal contact effects. To rationalize why the active site loop is closed in the absence of ligand in one of the subunits, extensive comparison with previously solved TIM structures was carried out, supported by the bulk of available experimental information about enzyme kinetics and reaction mechanism of TIM. The observation of both open and closed lid conformations in TIM crystals might be related to a persistent conformational heterogeneity of this protein in solution.
+
[[Category: Large Structures]]
-
 
+
-
==About this Structure==
+
-
1R2R is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R2R OCA].
+
-
 
+
-
==Reference==
+
-
Closed conformation of the active site loop of rabbit muscle triosephosphate isomerase in the absence of substrate: evidence of conformational heterogeneity., Aparicio R, Ferreira ST, Polikarpov I, J Mol Biol. 2003 Dec 12;334(5):1023-41. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14643664 14643664]
+
[[Category: Oryctolagus cuniculus]]
[[Category: Oryctolagus cuniculus]]
-
[[Category: Single protein]]
+
[[Category: Aparicio R]]
-
[[Category: Triose-phosphate isomerase]]
+
[[Category: Ferreira ST]]
-
[[Category: Aparicio, R.]]
+
[[Category: Polikarpov I]]
-
[[Category: Ferreira, S T.]]
+
-
[[Category: Polikarpov, I.]]
+
-
[[Category: closed loop conformation in the ligand-free state]]
+
-
[[Category: conformational heterogeneity]]
+
-
[[Category: tim]]
+
-
[[Category: tim-barrel]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:22:28 2008''
+

Current revision

CRYSTAL STRUCTURE OF RABBIT MUSCLE TRIOSEPHOSPHATE ISOMERASE

PDB ID 1r2r

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/1r2r"
Personal tools