1xrj

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:52, 14 February 2024) (edit) (undo)
 
Line 3: Line 3:
<StructureSection load='1xrj' size='340' side='right'caption='[[1xrj]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='1xrj' size='340' side='right'caption='[[1xrj]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[1xrj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XRJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1XRJ FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[1xrj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XRJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XRJ FirstGlance]. <br>
-
</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=C5P:CYTIDINE-5-MONOPHOSPHATE'>C5P</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+
</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&#8491;</td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1udw|1udw]], [[1uei|1uei]], [[1uej|1uej]], [[1ufq|1ufq]], [[1uj2|1uj2]]</div></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=C5P:CYTIDINE-5-MONOPHOSPHATE'>C5P</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">UCK2, UMPK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=1xrj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xrj OCA], [https://pdbe.org/1xrj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xrj RCSB], [https://www.ebi.ac.uk/pdbsum/1xrj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xrj ProSAT]</span></td></tr>
-
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uridine_kinase Uridine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.48 2.7.1.48] </span></td></tr>
+
-
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1xrj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xrj OCA], [http://pdbe.org/1xrj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xrj RCSB], [http://www.ebi.ac.uk/pdbsum/1xrj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xrj ProSAT]</span></td></tr>
+
</table>
</table>
== Function ==
== Function ==
-
[[http://www.uniprot.org/uniprot/UCK2_HUMAN UCK2_HUMAN]] Phosphorylates uridine and cytidine to uridine monophosphate and cytidine monophosphate. Does not phosphorylate deoxyribonucleosides or purine ribonucleosides. Can use ATP or GTP as a phosphate donor. Can also phosphorylate cytidine and uridine nucleoside analogs such as 6-azauridine, 5-fluorouridine, 4-thiouridine, 5-bromouridine, N(4)-acetylcytidine, N(4)-benzoylcytidine, 5-fluorocytidine, 2-thiocytidine, 5-methylcytidine, and N(4)-anisoylcytidine.
+
[https://www.uniprot.org/uniprot/UCK2_HUMAN UCK2_HUMAN] Phosphorylates uridine and cytidine to uridine monophosphate and cytidine monophosphate. Does not phosphorylate deoxyribonucleosides or purine ribonucleosides. Can use ATP or GTP as a phosphate donor. Can also phosphorylate cytidine and uridine nucleoside analogs such as 6-azauridine, 5-fluorouridine, 4-thiouridine, 5-bromouridine, N(4)-acetylcytidine, N(4)-benzoylcytidine, 5-fluorocytidine, 2-thiocytidine, 5-methylcytidine, and N(4)-anisoylcytidine.
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Line 22: Line 20:
</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=1xrj ConSurf].
</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=1xrj ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
-
<div style="background-color:#fffaf0;">
 
-
== Publication Abstract from PubMed ==
 
-
Uridine-cytidine nucleoside kinase 2 (UCK2) is the rate-limiting enzyme in the pyrimidine-nucleotide salvage pathway. UCK2 catalyzes the phosphorylation of the natural ribonucleosides cytidine and uridine to cytidine 5'-monophosphate (CMP) and uridine 5'-monophosphate (UMP), respectively, and activates several important frontline antimetabolite drugs. The present contribution reports the rapid crystal structure determination of human UCK2 complexed with a magnesium ion and the reaction products adenosine 5'-diphosphate (ADP) and CMP. Diffraction data were collected on a copper rotating-anode X-ray generator from one native UCK2 crystal and a single samarium-derivative crystal. Utilizing the relatively high anomalous signal from the samarium derivative at the Cu Kalpha wavelength, the structure was determined by single isomorphous replacement and single anomalous signal (SIRAS) phasing techniques. Two of the four major samarium sites are located in the active sites of the two UCK2 molecules that form the asymmetric unit and appear to displace the magnesium ions present in the native crystals. The crystal structures of UCK2 alone and in complex with various ligands have recently been determined using traditional multiple isomorphous replacement (MIR) phasing techniques and data from three heavy-atom derivatives. The reported structures validate our independently determined structure. Of more than 1000 kinase crystal structure entries in the Protein Data Bank, less than 1% of them have been determined by SIRAS. For the published kinase crystal structures determined by SIRAS, all data were reportedly collected at various synchrotron-radiation facilities. This study demonstrates that diffraction data collected from a single samarium derivative using Cu Kalpha radiation provides sufficient phasing power to determine a novel macromolecular crystal structure.
 
- 
-
Structure of human uridine-cytidine kinase 2 determined by SIRAS using a rotating-anode X-ray generator and a single samarium derivative.,Appleby TC, Larson G, Cheney IW, Walker H, Wu JZ, Zhong W, Hong Z, Yao N Acta Crystallogr D Biol Crystallogr. 2005 Mar;61(Pt 3):278-84. Epub 2005, Feb 24. PMID:15735337<ref>PMID:15735337</ref>
 
- 
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
-
</div>
 
-
<div class="pdbe-citations 1xrj" style="background-color:#fffaf0;"></div>
 
-
== References ==
 
-
<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Human]]
+
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Large Structures]]
-
[[Category: Uridine kinase]]
+
[[Category: Appleby TC]]
-
[[Category: Appleby, T C]]
+
[[Category: Cheney IW]]
-
[[Category: Cheney, I W]]
+
[[Category: Hong Z]]
-
[[Category: Hong, Z]]
+
[[Category: Larson G]]
-
[[Category: Larson, G]]
+
[[Category: Wu JZ]]
-
[[Category: Wu, J Z]]
+
[[Category: Yao N]]
-
[[Category: Yao, N]]
+
-
[[Category: Anomalous]]
+
-
[[Category: Anti-cancer]]
+
-
[[Category: Cancer]]
+
-
[[Category: Nucleoside kinase]]
+
-
[[Category: Oncology]]
+
-
[[Category: Rapid phasing]]
+
-
[[Category: Sad]]
+
-
[[Category: Samarium]]
+
-
[[Category: Single-wavelength]]
+
-
[[Category: Sira]]
+
-
[[Category: Transferase]]
+
-
[[Category: Uck2]]
+
-
[[Category: Uridine-cytidine kinase]]
+

Current revision

Rapid structure determination of human uridine-cytidine kinase 2 using a conventional laboratory X-ray source and a single samarium derivative

PDB ID 1xrj

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Personal tools