2j4l: Difference between revisions

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<StructureSection load='2j4l' size='340' side='right'caption='[[2j4l]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
<StructureSection load='2j4l' size='340' side='right'caption='[[2j4l]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2j4l]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_35091 Atcc 35091]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J4L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2J4L FirstGlance]. <br>
<table><tr><td colspan='2'>[[2j4l]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus Saccharolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J4L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2J4L FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UTP:URIDINE+5-TRIPHOSPHATE'>UTP</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]] 2.8&#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]], [[2j4k|2j4k]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UTP:URIDINE+5-TRIPHOSPHATE'>UTP</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=2j4l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j4l OCA], [https://pdbe.org/2j4l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2j4l RCSB], [https://www.ebi.ac.uk/pdbsum/2j4l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2j4l 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=2j4l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j4l OCA], [https://pdbe.org/2j4l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2j4l RCSB], [https://www.ebi.ac.uk/pdbsum/2j4l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2j4l 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]]
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</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=2j4l 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=2j4l ConSurf].
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<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 2j4l" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Atcc 35091]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: UMP kinase]]
[[Category: Saccharolobus solfataricus]]
[[Category: Jensen, K F]]
[[Category: Jensen KF]]
[[Category: Jensen, K S]]
[[Category: Jensen KS]]
[[Category: Johansson, E]]
[[Category: Johansson E]]
[[Category: Aspartokinase fold]]
[[Category: Nucleoside monophosphate kinase]]
[[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 UTP to 2.8 Angstrom resolutionCrystal structure of uridylate kinase from Sulfolobus solfataricus in complex with UTP to 2.8 Angstrom resolution

Structural highlights

2j4l is a 12 chain structure with sequence from Saccharolobus solfataricus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.8Å
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

2j4l, resolution 2.80Å

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