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.


1did

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:54, 7 February 2024) (edit) (undo)
 
(14 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1did.jpg|left|200px]]
 
-
{{Structure
+
==OBSERVATIONS OF REACTION INTERMEDIATES AND THE MECHANISM OF ALDOSE-KETOSE INTERCONVERSION BY D-XYLOSE ISOMERASE==
-
|PDB= 1did |SIZE=350|CAPTION= <scene name='initialview01'>1did</scene>, resolution 2.5&Aring;
+
<StructureSection load='1did' size='340' side='right'caption='[[1did]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=DIG:2,5-DIDEOXY-2,5-IMINO-D-GLUCITOL'>DIG</scene> and <scene name='pdbligand=MN:MANGANESE (II) ION'>MN</scene>
+
<table><tr><td colspan='2'>[[1did]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arthrobacter_sp._NRRL_B3728 Arthrobacter sp. NRRL B3728]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DID OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DID FirstGlance]. <br>
-
|ACTIVITY= [http://en.wikipedia.org/wiki/Xylose_isomerase Xylose isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.5 5.3.1.5]
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
-
|GENE=
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DIG:2,5-DIDEOXY-2,5-IMINO-D-GLUCITOL'>DIG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=1did FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1did OCA], [https://pdbe.org/1did PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1did RCSB], [https://www.ebi.ac.uk/pdbsum/1did PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1did ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/XYLA_ARTS7 XYLA_ARTS7]
 +
== 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/di/1did_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=1did ConSurf].
 +
<div style="clear:both"></div>
-
'''OBSERVATIONS OF REACTION INTERMEDIATES AND THE MECHANISM OF ALDOSE-KETOSE INTERCONVERSION BY D-XYLOSE ISOMERASE'''
+
==See Also==
-
 
+
*[[D-xylose isomerase 3D structures|D-xylose isomerase 3D structures]]
-
 
+
__TOC__
-
==Overview==
+
</StructureSection>
-
Crystallographic studies of D-xylose isomerase (D-xylose ketol-isomerase, EC 5.3.1.5) incubated to equilibrium with substrate/product mixtures of xylose and xylulose show electron density for a bound intermediate. The accumulation of this bound intermediate shows that the mechanism is a non-Michaelis type. Carrell et al. [Carrell, H. L., Glusker, J. P., Burger, V., Manfre, F., Tritsch, D. &amp; Biellmann, J.-F. (1989) Proc. Natl. Acad. Sci. USA 86, 4440-4444] and the present authors studied crystals of the enzyme-substrate complex under different conditions and made different interpretations of the substrate density, leading to different conclusions about the enzyme mechanism. All authors agree that the bound intermediate of the sugar is in an open-chain form. It is suggested that the higher-temperature study of Carrell et al. may have produced an equilibrium of multiple states, whose density fits poorly to the open-chain substrate, and led to incorrect interpretation. The two groups also bound different closed-ring sugar analogues to the enzyme, but these analogues bind differently. A possible explanation consistent with all the data is that the enzyme operates by a hydride shift mechanism.
+
[[Category: Arthrobacter sp. NRRL B3728]]
-
 
+
[[Category: Large Structures]]
-
==About this Structure==
+
[[Category: Blow DM]]
-
1DID is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Arthrobacter_sp. Arthrobacter sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DID OCA].
+
[[Category: Collyer CA]]
-
 
+
[[Category: Goldberg JD]]
-
==Reference==
+
-
Observations of reaction intermediates and the mechanism of aldose-ketose interconversion by D-xylose isomerase., Collyer CA, Blow DM, Proc Natl Acad Sci U S A. 1990 Feb;87(4):1362-6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/2304904 2304904]
+
-
[[Category: Arthrobacter sp.]]
+
-
[[Category: Single protein]]
+
-
[[Category: Xylose isomerase]]
+
-
[[Category: Blow, D M.]]
+
-
[[Category: Collyer, C A.]]
+
-
[[Category: Goldberg, J D.]]
+
-
[[Category: DIG]]
+
-
[[Category: MN]]
+
-
[[Category: isomerase(intramolecular oxidoreductse)]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:38:54 2008''
+

Current revision

OBSERVATIONS OF REACTION INTERMEDIATES AND THE MECHANISM OF ALDOSE-KETOSE INTERCONVERSION BY D-XYLOSE ISOMERASE

PDB ID 1did

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/1did"
Personal tools