2uyt

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:47, 9 October 2024) (edit) (undo)
 
(16 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2uyt.gif|left|200px]]<br /><applet load="2uyt" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="2uyt, resolution 1.55&Aring;" />
 
-
'''STRUCTURE OF L-RHAMNULOSE KINASE IN COMPLEX WITH ADP AND BETA-L-RHAMNULOSE.'''<br />
 
-
==Overview==
+
==Structure of L-rhamnulose kinase in complex with ADP and beta-L- rhamnulose.==
-
The enzyme L-rhamnulose kinase from Escherichia coli participates in the, degradation pathway of L-rhamnose, a common natural deoxy-hexose. The, structure of the enzyme in a ternary complex with its substrates ADP and, L-rhamnulose has been determined at 1.55A resolution and refined to, R(cryst)/R(free) values of 0.179/0.209. The result was compared with the, lower resolution structure of a corresponding complex containing, L-fructose instead of L-rhamnulose. In light of the two established sugar, positions and conformations, a number of rare sugars have been modeled, into the active center of L-rhamnulose kinase and the model structures, have been compared with the known enzymatic phosphorylation rates. Rare, sugars are of rising interest for the synthesis of bioactive compounds.
+
<StructureSection load='2uyt' size='340' side='right'caption='[[2uyt]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[2uyt]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_BL21(DE3) Escherichia coli BL21(DE3)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2UYT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2UYT FirstGlance]. <br>
 +
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.55&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=LRH:6-DEOXY-BETA-L-FRUCTOFURANOSE'>LRH</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=2uyt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2uyt OCA], [https://pdbe.org/2uyt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2uyt RCSB], [https://www.ebi.ac.uk/pdbsum/2uyt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2uyt ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/RHAB_ECOUT RHAB_ECOUT] Involved in the catabolism of L-rhamnose (6-deoxy-L-mannose). It could also play a role in the metabolism of some rare sugars such as L-fructose. Catalyzes the transfer of the gamma-phosphate group from ATP to the 1-hydroxyl group of L-rhamnulose to yield L-rhamnulose 1-phosphate. It can also phosphorylate L-fuculose and L-xylulose. It requires the R-configuration at the C-3 atom.[HAMAP-Rule:MF_01535]<ref>PMID:17568582</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/uy/2uyt_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2uyt ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The enzyme L-rhamnulose kinase from Escherichia coli participates in the degradation pathway of L-rhamnose, a common natural deoxy-hexose. The structure of the enzyme in a ternary complex with its substrates ADP and L-rhamnulose has been determined at 1.55A resolution and refined to R(cryst)/R(free) values of 0.179/0.209. The result was compared with the lower resolution structure of a corresponding complex containing L-fructose instead of L-rhamnulose. In light of the two established sugar positions and conformations, a number of rare sugars have been modeled into the active center of L-rhamnulose kinase and the model structures have been compared with the known enzymatic phosphorylation rates. Rare sugars are of rising interest for the synthesis of bioactive compounds.
-
==About this Structure==
+
Substrate spectrum of L-rhamnulose kinase related to models derived from two ternary complex structures.,Grueninger D, Schulz GE FEBS Lett. 2007 Jun 26;581(16):3127-30. Epub 2007 Jun 6. PMID:17568582<ref>PMID:17568582</ref>
-
2UYT is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=LRH:'>LRH</scene> and <scene name='pdbligand=ADP:'>ADP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Rhamnulokinase Rhamnulokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.5 2.7.1.5] Known structural/functional Site: <scene name='pdbsite=AC1:Adp+Binding+Site+For+Chain+A'>AC1</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2UYT OCA].
+
-
==Reference==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
Substrate spectrum of L-rhamnulose kinase related to models derived from two ternary complex structures., Grueninger D, Schulz GE, FEBS Lett. 2007 Jun 26;581(16):3127-30. Epub 2007 Jun 6. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17568582 17568582]
+
</div>
-
[[Category: Escherichia coli]]
+
<div class="pdbe-citations 2uyt" style="background-color:#fffaf0;"></div>
-
[[Category: Rhamnulokinase]]
+
== References ==
-
[[Category: Single protein]]
+
<references/>
-
[[Category: Grueninger, D.]]
+
__TOC__
-
[[Category: Schulz, G.E.]]
+
</StructureSection>
-
[[Category: ADP]]
+
[[Category: Large Structures]]
-
[[Category: LRH]]
+
[[Category: Grueninger D]]
-
[[Category: hexokinase-hsp70- actin superfamily]]
+
[[Category: Schulz GE]]
-
[[Category: in-line phosphoryl transfer]]
+
-
[[Category: induced fit]]
+
-
[[Category: kinase]]
+
-
[[Category: l-rhamnulose kinase]]
+
-
[[Category: rare sugars]]
+
-
[[Category: rhamnose degradation]]
+
-
[[Category: rhamnose metabolism]]
+
-
[[Category: transferase]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Feb 3 10:48:30 2008''
+

Current revision

Structure of L-rhamnulose kinase in complex with ADP and beta-L- rhamnulose.

PDB ID 2uyt

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/2uyt"
Personal tools