2zf5: Difference between revisions

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{{Seed}}
[[Image:2zf5.png|left|200px]]


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==Crystal Structure of highly thermostable glycerol kinase from a hyperthermophilic archaeon==
The line below this paragraph, containing "STRUCTURE_2zf5", creates the "Structure Box" on the page.
<StructureSection load='2zf5' size='340' side='right'caption='[[2zf5]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2zf5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis_KOD1 Thermococcus kodakarensis KOD1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZF5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZF5 FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2zf5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zf5 OCA], [https://pdbe.org/2zf5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zf5 RCSB], [https://www.ebi.ac.uk/pdbsum/2zf5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zf5 ProSAT]</span></td></tr>
{{STRUCTURE_2zf5|  PDB=2zf5  |  SCENE=  }}
</table>
== Function ==
[https://www.uniprot.org/uniprot/GLPK_THEKO GLPK_THEKO] Key enzyme in the regulation of glycerol uptake and metabolism. Catalyzes the phosphorylation of glycerol to yield sn-glycerol 3-phosphate. Can utilize other nucleoside triphosphates (GTP, CTP, UTP AND ITP) as a phosphoryl donor.[HAMAP-Rule:MF_00186]<ref>PMID:9930671</ref>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zf/2zf5_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </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/main_output.php?pdb_ID=2zf5 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The crystal structure of glycerol kinase from the hyperthermophilic archaeon Thermococcus kodakaraensis (Tk-GK) in a dimeric form was determined at a resolution of 2.4 A. This is the first crystal structure of a hyperthermophilic glycerol kinase. The overall structure of the Tk-GK dimer is very similar to that of the Escherichia coli glycerol kinase (Ec-GK) dimer. However, two dimers of Ec-GK can associate into a tetramer with a twofold axis, whereas those of Tk-GK cannot. This may be the reason why Tk-GK is not inhibited by fructose 1,6-bisphosphate, because the fructose 1,6-bisphosphate binding site is produced only when a tetrameric structure is formed. Differential scanning calorimetry analyses indicate that Tk-GK is a highly thermostable protein with a melting temperature (T(m)) of 105.4 degrees C for the major transition. This value is higher than that of Ec-GK by 34.1 degrees C. Comparison of the crystal structures of Tk-GK and Ec-GK indicate that there is a marked difference in the number of ion pairs in the alpha16 helix. Four ion pairs, termed IP1-IP4, are formed in this helix in the Tk-GK structure. To examine whether these ion pairs contribute to the stabilization of Tk-GK, four Tk-GK and four Ec-GK derivatives with reciprocal mutations at the IP1-IP4 sites were constructed. The determination of their stabilities indicates that the removal of each ion pair does not affect the stability of Tk-GK significantly, whereas the mutations designed to introduce one of these ion pairs stabilize or destabilize Ec-GK considerably. These results suggest that the ion pairs in the alpha16 helix contribute to the stabilization of Tk-GK in a cooperative manner.


===Crystal Structure of highly thermostable glycerol kinase from a hyperthermophilic archaeon===
Crystal structure of highly thermostable glycerol kinase from a hyperthermophilic archaeon in a dimeric form.,Koga Y, Katsumi R, You DJ, Matsumura H, Takano K, Kanaya S FEBS J. 2008 May;275(10):2632-43. Epub 2008 Apr 17. PMID:18422647<ref>PMID:18422647</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2zf5" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_18422647}}, adds the Publication Abstract to the page
*[[Glycerol kinase|Glycerol kinase]]
(as it appears on PubMed at http://www.pubmed.gov), where 18422647 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_18422647}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
2ZF5 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermococcus_kodakarensis Thermococcus kodakarensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZF5 OCA].
[[Category: Thermococcus kodakarensis KOD1]]
 
[[Category: Kanaya S]]
==Reference==
[[Category: Katsumi R]]
Crystal structure of highly thermostable glycerol kinase from a hyperthermophilic archaeon in a dimeric form., Koga Y, Katsumi R, You DJ, Matsumura H, Takano K, Kanaya S, FEBS J. 2008 May;275(10):2632-43. Epub 2008 Apr 17. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18422647 18422647]
[[Category: Koga Y]]
[[Category: Glycerol kinase]]
[[Category: Matsumura H]]
[[Category: Single protein]]
[[Category: Takano K]]
[[Category: Thermococcus kodakarensis]]
[[Category: You D-J]]
[[Category: Kanaya, S.]]
[[Category: Katsumi, R.]]
[[Category: Koga, Y.]]
[[Category: Matsumura, H.]]
[[Category: Takano, K.]]
[[Category: You, D J.]]
[[Category: Atp-binding]]
[[Category: Glycerol kinase]]
[[Category: Glycerol metabolism]]
[[Category: Hyperthermophilic archaeon]]
[[Category: Nucleotide-binding]]
[[Category: Transferase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 11:55:09 2008''

Latest revision as of 13:34, 1 November 2023

Crystal Structure of highly thermostable glycerol kinase from a hyperthermophilic archaeon

2zf5, resolution 2.40Å

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