2j4k: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
Line 3: Line 3:
<StructureSection load='2j4k' size='340' side='right'caption='[[2j4k]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
<StructureSection load='2j4k' size='340' side='right'caption='[[2j4k]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2j4k]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Sacs2 Sacs2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J4K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2J4K FirstGlance]. <br>
<table><tr><td colspan='2'>[[2j4k]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus_P2 Saccharolobus solfataricus P2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J4K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2J4K FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=U5P:URIDINE-5-MONOPHOSPHATE'>U5P</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]] 2.2&#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;'>[[2j4j|2j4j]], [[2j4l|2j4l]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=U5P:URIDINE-5-MONOPHOSPHATE'>U5P</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/UMP_kinase UMP kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.22 2.7.4.22] </span></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=2j4k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j4k OCA], [https://pdbe.org/2j4k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2j4k RCSB], [https://www.ebi.ac.uk/pdbsum/2j4k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2j4k ProSAT]</span></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=2j4k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j4k OCA], [https://pdbe.org/2j4k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2j4k RCSB], [https://www.ebi.ac.uk/pdbsum/2j4k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2j4k ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/PYRH_SULSO PYRH_SULSO]] Catalyzes the reversible phosphorylation of UMP to UDP, with ATP as the most efficient phosphate donor. Is also able to phosphorylate dUMP, although much less efficiently.<ref>PMID:17297917</ref>
[https://www.uniprot.org/uniprot/PYRH_SACS2 PYRH_SACS2] Catalyzes the reversible phosphorylation of UMP to UDP, with ATP as the most efficient phosphate donor. Is also able to phosphorylate dUMP, although much less efficiently.<ref>PMID:17297917</ref>  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Line 21: 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=2j4k 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=2j4k ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The pyrH gene encoding uridylate kinase (UMPK) from the extreme thermoacidophilic archaeon Sulfolobus solfataricus was cloned and expressed in Escherichia coli, and the enzyme (SsUMPK) was purified. Size exclusion chromatography and sedimentation experiments showed that the oligomeric state in solution is hexameric. SsUMPK shows maximum catalytic rate at pH 7.0, and variation of pH only influences the turnover number. Catalysis proceeds by a sequential reaction mechanism of random order and depends on a divalent cation. The enzyme exhibits high substrate specificity toward UMP and ATP and is inhibited by UTP, whereas CTP and GTP do not influence activity. UTP binds to the enzyme with a sigmoid binding curve, whereas GTP does not bind. The crystal structure of SsUMPK was determined for three different complexes, a ternary complex with UMP and the nonhydrolyzable ATP analogue beta,gamma-methylene-ATP, a complex with UMP, and a complex with UTP to 2.1, 2.2, and 2.8 A resolution, respectively. One UTP molecule was bound in the acceptor site per subunit, leading to the exclusion of both substrates from the active site. In all cases, SsUMPK crystallized as a hexamer with the main fold shared with other prokaryotic UMPKs. Similar to UMPK from Pyrococcus furiosus, SsUMPK has an active site enclosing loop. This loop was only ordered in one subunit in the ternary complex, which also contained an unusual arrangement of ligands (possibly a dinucleotide) in the active site and an altered orientation of the catalytic residue Arg48 relative to the other five subunits of the hexamer.
Structural and enzymatic investigation of the Sulfolobus solfataricus uridylate kinase shows competitive UTP inhibition and the lack of GTP stimulation.,Jensen KS, Johansson E, Jensen KF Biochemistry. 2007 Mar 13;46(10):2745-57. Epub 2007 Feb 13. PMID:17297917<ref>PMID:17297917</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2j4k" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
Line 38: Line 28:
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Sacs2]]
[[Category: Saccharolobus solfataricus P2]]
[[Category: UMP kinase]]
[[Category: Jensen KF]]
[[Category: Jensen, K F]]
[[Category: Jensen KS]]
[[Category: Jensen, K S]]
[[Category: Johansson E]]
[[Category: Johansson, E]]
[[Category: Aspartokinase family]]
[[Category: Kinase]]
[[Category: Nucleoside monophosphate kinase]]
[[Category: Pyrimidine biosynthesis]]
[[Category: Pyrimidine nucleotide synthesis]]
[[Category: Transferase]]
[[Category: Ump kinase]]

Latest revision as of 09:41, 1 May 2024

Crystal structure of uridylate kinase from Sulfolobus solfataricus in complex with UMP to 2.2 Angstrom resolutionCrystal structure of uridylate kinase from Sulfolobus solfataricus in complex with UMP to 2.2 Angstrom resolution

Structural highlights

2j4k is a 6 chain structure with sequence from Saccharolobus solfataricus P2. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.2Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PYRH_SACS2 Catalyzes the reversible phosphorylation of UMP to UDP, with ATP as the most efficient phosphate donor. Is also able to phosphorylate dUMP, although much less efficiently.[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  1. ↑ Jensen KS, Johansson E, Jensen KF. Structural and enzymatic investigation of the Sulfolobus solfataricus uridylate kinase shows competitive UTP inhibition and the lack of GTP stimulation. Biochemistry. 2007 Mar 13;46(10):2745-57. Epub 2007 Feb 13. PMID:17297917 doi:10.1021/bi0618159

2j4k, resolution 2.20Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=2j4k&oldid=4135564"