3ek6: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(3 intermediate revisions by the same user not shown)
Line 1: Line 1:
==Unique GTP-binding Pocket and Allostery of UMP Kinase from a Gram-Negative Phytopathogen Bacterium==
==Unique GTP-binding Pocket and Allostery of UMP Kinase from a Gram-Negative Phytopathogen Bacterium==
<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 [http://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 [http://oca.weizmann.ac.il/oca-docs/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">[[3ek5|3ek5]]</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 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=340 Xanthomonas campestris pv. campestris])</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UMP_kinase UMP kinase], with EC number [http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ek6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ek6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ek6 RCSB], [http://www.ebi.ac.uk/pdbsum/3ek6 PDBsum]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://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]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ek/3ek6_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ek/3ek6_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </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].
</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>


==See Also==
==See Also==
*[[Uridylate kinase|Uridylate kinase]]
*[[Uridylate kinase|Uridylate kinase]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: UMP kinase]]
[[Category: Large Structures]]
[[Category: Xanthomonas campestris pv. campestris]]
[[Category: Xanthomonas campestris pv. campestris]]
[[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, A H.J]]
[[Category: Wang AH-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

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=3ek6&oldid=4103598"