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.


1orr

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:02, 14 February 2024) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1orr.jpg|left|200px]]
 
-
<!--
+
==Crystal Structure of CDP-Tyvelose 2-Epimerase complexed with NAD and CDP==
-
The line below this paragraph, containing "STRUCTURE_1orr", creates the "Structure Box" on the page.
+
<StructureSection load='1orr' size='340' side='right'caption='[[1orr]], [[Resolution|resolution]] 1.50&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'>[[1orr]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhi Salmonella enterica subsp. enterica serovar Typhi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ORR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ORR 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]] 1.5&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CDP:CYTIDINE-5-DIPHOSPHATE'>CDP</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-
{{STRUCTURE_1orr| PDB=1orr | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1orr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1orr OCA], [https://pdbe.org/1orr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1orr RCSB], [https://www.ebi.ac.uk/pdbsum/1orr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1orr ProSAT]</span></td></tr>
-
 
+
</table>
-
'''Crystal Structure of CDP-Tyvelose 2-Epimerase complexed with NAD and CDP'''
+
== Function ==
-
 
+
[https://www.uniprot.org/uniprot/RFBE_SALTI RFBE_SALTI] Catalyzes the isomeration of CDP-paratose to CDP-tyvelose.
-
 
+
== Evolutionary Conservation ==
-
==Overview==
+
[[Image:Consurf_key_small.gif|200px|right]]
-
Tyvelose epimerase catalyzes the last step in the biosynthesis of tyvelose by converting CDP-d-paratose to CDP-d-tyvelose. This unusual 3,6-dideoxyhexose occurs in the O-antigens of some types of Gram-negative bacteria. Here we describe the cloning, protein purification, and high-resolution x-ray crystallographic analysis of tyvelose epimerase from Salmonella typhi complexed with CDP. The enzyme from S. typhi is a homotetramer with each subunit containing 339 amino acid residues and a tightly bound NAD+ cofactor. The quaternary structure of the enzyme displays 222 symmetry and can be aptly described as a dimer of dimers. Each subunit folds into two distinct lobes: the N-terminal motif responsible for NAD+ binding and the C-terminal region that harbors the binding site for CDP. The analysis described here demonstrates that tyvelose epimerase belongs to the short-chain dehydrogenase/reductase superfamily of enzymes. Indeed, its active site is reminiscent to that observed for UDP-galactose 4-epimerase, an enzyme that plays a key role in galactose metabolism. Unlike UDP-galactose 4-epimerase where the conversion of configuration occurs about C-4 of the UDP-glucose or UDP-galactose substrates, in the reaction catalyzed by tyvelose epimerase, the inversion of stereochemistry occurs at C-2. On the basis of the observed binding mode for CDP, it is possible to predict the manner in which the substrate, CDP-paratose, and the product, CDP-tyvelose, might be accommodated within the active site of tyvelose epimerase.
+
Check<jmol>
-
 
+
<jmolCheckbox>
-
==About this Structure==
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/or/1orr_consurf.spt"</scriptWhenChecked>
-
1ORR is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Salmonella_typhi Salmonella typhi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ORR OCA].
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
 
+
<text>to colour the structure by Evolutionary Conservation</text>
-
==Reference==
+
</jmolCheckbox>
-
High resolution x-ray structure of tyvelose epimerase from Salmonella typhi., Koropatkin NM, Liu HW, Holden HM, J Biol Chem. 2003 Jun 6;278(23):20874-81. Epub 2003 Mar 17. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12642575 12642575]
+
</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=1orr ConSurf].
-
[[Category: Salmonella typhi]]
+
<div style="clear:both"></div>
-
[[Category: Single protein]]
+
__TOC__
-
[[Category: Holden, H M.]]
+
</StructureSection>
-
[[Category: Koropatkin, N M.]]
+
[[Category: Large Structures]]
-
[[Category: Liu, H.]]
+
[[Category: Salmonella enterica subsp. enterica serovar Typhi]]
-
[[Category: Rossmann fold]]
+
[[Category: Holden HM]]
-
[[Category: Short-chain dehydrogenase/reductase]]
+
[[Category: Koropatkin NM]]
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 04:12:13 2008''
+
[[Category: Liu H]]

Current revision

Crystal Structure of CDP-Tyvelose 2-Epimerase complexed with NAD and CDP

PDB ID 1orr

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/1orr"
Personal tools