4ukd: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
==UMP/CMP KINASE FROM SLIME MOLD COMPLEXED WITH ADP, UDP, BERYLLIUM FLUORIDE== | |||
[[Image: | <StructureSection load='4ukd' size='340' side='right' caption='[[4ukd]], [[Resolution|resolution]] 2.00Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4ukd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UKD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UKD FirstGlance]. <br> | |||
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=BF2:BERYLLIUM+DIFLUORIDE'>BF2</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene><br> | |||
<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">KCY_DICDI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=44689 Dictyostelium discoideum])</td></tr> | |||
<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr> | |||
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ukd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ukd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ukd RCSB], [http://www.ebi.ac.uk/pdbsum/4ukd PDBsum]</span></td></tr> | |||
<table> | |||
== 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/4ukd_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/chain_selection.php?pdb_ID=2ata ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
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. | |||
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:9280438<ref>PMID:9280438</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | |||
< | |||
[[Category: Cytidylate kinase]] | [[Category: Cytidylate kinase]] | ||
[[Category: Dictyostelium discoideum]] | [[Category: Dictyostelium discoideum]] | ||
| Line 33: | Line 39: | ||
[[Category: Transferase]] | [[Category: Transferase]] | ||
[[Category: Transition state analog complex]] | [[Category: Transition state analog complex]] | ||
Revision as of 11:37, 5 June 2014
UMP/CMP KINASE FROM SLIME MOLD COMPLEXED WITH ADP, UDP, BERYLLIUM FLUORIDEUMP/CMP KINASE FROM SLIME MOLD COMPLEXED WITH ADP, UDP, BERYLLIUM FLUORIDE
Structural highlights
Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedUMP/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. 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:9280438[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
|
| ||||||||||||||||||||