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.


3ukd

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (10:24, 1 March 2024) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:3ukd.gif|left|200px]]<br /><applet load="3ukd" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="3ukd, resolution 1.9&Aring;" />
 
-
'''UMP/CMP KINASE FROM SLIME MOLD COMPLEXED WITH ADP, CMP, AND ALF3'''<br />
 
-
==Overview==
+
==UMP/CMP KINASE FROM SLIME MOLD COMPLEXED WITH ADP, CMP, AND ALF3==
-
UMP/CMP kinase from Dictyostelium discoideum (UmpKdicty) catalyzes the specific transfer of the terminal phosphate of ATP to UMP or CMP. Crystal structures of UmpKdicty with substrates and the transition state analogs AlF3 or BeF2 that lock UmpKdicty in active conformations were solved. The positions of the catalytic Mg2+ and the highly conserved lysine of the P loop are virtually invariant in the different structures. In contrast, catalytic arginines move to stabilize charges that develop during this reaction. The location of the arginines indicates formation of negative charges during the reaction at the transferred phosphoryl group, but not at the phosphate bridging oxygen atoms. This is consistent with an associative phosphoryl transfer mechanism but not with a dissociative one.
+
<StructureSection load='3ukd' size='340' side='right'caption='[[3ukd]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[3ukd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UKD 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]] 1.9&#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=AF3:ALUMINUM+FLUORIDE'>AF3</scene>, <scene name='pdbligand=C5P:CYTIDINE-5-MONOPHOSPHATE'>C5P</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=3ukd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ukd OCA], [https://pdbe.org/3ukd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ukd RCSB], [https://www.ebi.ac.uk/pdbsum/3ukd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ukd ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/KCY_DICDI KCY_DICDI] This UMP-CMP kinase uses preferentially ATP as phosphate donor and is specific for UMP and CMP.
 +
== 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/uk/3ukd_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=3ukd ConSurf].
 +
<div style="clear:both"></div>
-
==About this Structure==
+
==See Also==
-
3UKD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum] with <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=ADP:'>ADP</scene>, <scene name='pdbligand=C5P:'>C5P</scene> and <scene name='pdbligand=AF3:'>AF3</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Cytidylate_kinase Cytidylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.14 2.7.4.14] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UKD OCA].
+
*[[UMP/CMP kinase|UMP/CMP kinase]]
-
 
+
__TOC__
-
==Reference==
+
</StructureSection>
-
Structures of active conformations of UMP kinase from Dictyostelium discoideum suggest phosphoryl transfer is associative., Schlichting I, Reinstein J, Biochemistry. 1997 Aug 5;36(31):9290-6. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9280438 9280438]
+
-
[[Category: Cytidylate kinase]]
+
[[Category: Dictyostelium discoideum]]
[[Category: Dictyostelium discoideum]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Reinstein, J.]]
+
[[Category: Reinstein J]]
-
[[Category: Schlichting, I.]]
+
[[Category: Schlichting I]]
-
[[Category: ADP]]
+
-
[[Category: AF3]]
+
-
[[Category: C5P]]
+
-
[[Category: MG]]
+
-
[[Category: nmp kinase]]
+
-
[[Category: nucleoside monophosphate kinase]]
+
-
[[Category: phosphoryl transfer]]
+
-
[[Category: transferase]]
+
-
[[Category: transition state analog complex]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:11:43 2008''
+

Current revision

UMP/CMP KINASE FROM SLIME MOLD COMPLEXED WITH ADP, CMP, AND ALF3

PDB ID 3ukd

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/3ukd"
Personal tools