3ek6: Difference between revisions

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<StructureSection load='3ek6' size='340' side='right'caption='[[3ek6]], [[Resolution|resolution]] 2.34&Aring;' scene=''>
<StructureSection load='3ek6' size='340' side='right'caption='[[3ek6]], [[Resolution|resolution]] 2.34&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3ek6]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Xance Xance]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EK6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EK6 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3ek6]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Xanthomonas_campestris_pv._campestris Xanthomonas campestris pv. campestris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EK6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EK6 FirstGlance]. <br>
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ek5|3ek5]]</div></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]] 2.34&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pyrH, XCC1371 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=340 XANCE])</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=3ek6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ek6 OCA], [https://pdbe.org/3ek6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ek6 RCSB], [https://www.ebi.ac.uk/pdbsum/3ek6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ek6 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=3ek6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ek6 OCA], [https://pdbe.org/3ek6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ek6 RCSB], [https://www.ebi.ac.uk/pdbsum/3ek6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ek6 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/PYRH_XANCP PYRH_XANCP]] Catalyzes the reversible phosphorylation of UMP to UDP (By similarity).  
[https://www.uniprot.org/uniprot/PYRH_XANCP PYRH_XANCP] Catalyzes the reversible phosphorylation of UMP to UDP (By similarity).
== 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=3ek6 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=3ek6 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Using X-ray diffraction methodology, we have successfully determined the tertiary structures of the apo- and GTP-bound forms of uridylate kinase (UMPK) from the Gram-negative plant pathogen Xanthomonas campestris with crystals grown under a strong magnetic field. The flexible ATP- and UMP-binding loops are clearly shown under this situation. X. campestris UMPK contains a unique patch of noticeably positive nature from residue R100 to residue R127, allowing it to form a special GTP-binding pocket in the central hole of the structure. Although GTP is found to be situated in a pocket similar to that of the ATP-binding pocket in Bacillus anthracis UMPK, superimposition between the two pockets indicates that they adopt very distinct conformations. Detailed structural analyses of X. campestris UMPK between its apo- and GTP-bound forms reveal that binding of GTP does not induce global conformational change for X. campestris UMPK and only moderates movements for the ATP- and UMP-binding loops. Binding of GTP effector seems to "heat up" X. campestris UMPK, causing overall increases of B-factors for the protein, except for residues interacting with the guanine base. Moderate increase of enzyme activity, as is the case detected in other Gram-negative bacteria, is observed for X. campestris UMPK in the presence of an allosteric GTP effector. Given that the GTP molecules bind in the central cavity of the hexamer and that each GTP molecule interacts with more than one monomer, it is likely that binding of GTP modifies the hexameric assembly to exert long-range allosteric control on X. campestris UMPK, similar to that suggested for the effect of ATP effector on B. anthracis UMPK.
Unique GTP-Binding Pocket and Allostery of Uridylate Kinase from a Gram-Negative Phytopathogenic Bacterium.,Tu JL, Chin KH, Wang AH, Chou SH J Mol Biol. 2008 Nov 25. PMID:19059268<ref>PMID:19059268</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3ek6" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Uridylate kinase|Uridylate kinase]]
*[[Uridylate kinase|Uridylate kinase]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: UMP kinase]]
[[Category: Xanthomonas campestris pv. campestris]]
[[Category: Xance]]
[[Category: Chin K-H]]
[[Category: Chin, K H]]
[[Category: Chou S-H]]
[[Category: Chou, S H]]
[[Category: Tu J-L]]
[[Category: Tu, J L]]
[[Category: Wang AH-J]]
[[Category: Wang, A H.J]]
[[Category: Allosteric regulation]]
[[Category: Atp-binding]]
[[Category: Kinase]]
[[Category: Nucleotide-binding]]
[[Category: Pyrimidine biosynthesis]]
[[Category: Transferase]]
[[Category: Umpk crystal structure]]
[[Category: Unique gtp binding site]]
[[Category: Xanthomonas campestri]]

Latest revision as of 11:25, 20 March 2024

Unique GTP-binding Pocket and Allostery of UMP Kinase from a Gram-Negative Phytopathogen BacteriumUnique GTP-binding Pocket and Allostery of UMP Kinase from a Gram-Negative Phytopathogen Bacterium

Structural highlights

3ek6 is a 6 chain structure with sequence from Xanthomonas campestris pv. campestris. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.34Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PYRH_XANCP Catalyzes the reversible phosphorylation of UMP to UDP (By similarity).

Evolutionary Conservation

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

See Also

3ek6, resolution 2.34Å

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