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2zf5

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{{Seed}}
 
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[[Image:2zf5.png|left|200px]]
 
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==Crystal Structure of highly thermostable glycerol kinase from a hyperthermophilic archaeon==
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The line below this paragraph, containing "STRUCTURE_2zf5", creates the "Structure Box" on the page.
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<StructureSection load='2zf5' size='340' side='right'caption='[[2zf5]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<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>
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or leave the SCENE parameter empty for the default display.
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</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>
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{{STRUCTURE_2zf5| PDB=2zf5 | SCENE= }}
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</table>
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== Function ==
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[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>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zf/2zf5_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=2zf5 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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===Crystal Structure of highly thermostable glycerol kinase from a hyperthermophilic archaeon===
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2zf5" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_18422647}}, adds the Publication Abstract to the page
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*[[Glycerol kinase|Glycerol kinase]]
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(as it appears on PubMed at http://www.pubmed.gov), where 18422647 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_18422647}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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2ZF5 is a 2 chains structure of sequences from [http://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].
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[[Category: Thermococcus kodakarensis KOD1]]
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[[Category: Kanaya S]]
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==Reference==
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[[Category: Katsumi R]]
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<ref group="xtra">PMID:18422647</ref><references group="xtra"/>
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[[Category: Koga Y]]
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[[Category: Glycerol kinase]]
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[[Category: Matsumura H]]
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[[Category: Thermococcus kodakarensis kod1]]
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[[Category: Takano K]]
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[[Category: Kanaya, S.]]
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[[Category: You D-J]]
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[[Category: Katsumi, R.]]
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[[Category: Koga, Y.]]
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[[Category: Matsumura, H.]]
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[[Category: Takano, K.]]
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[[Category: You, D J.]]
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[[Category: Atp-binding]]
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[[Category: Glycerol kinase]]
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[[Category: Glycerol metabolism]]
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[[Category: Hyperthermophilic archaeon]]
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[[Category: Nucleotide-binding]]
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[[Category: Transferase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 9 08:56:13 2009''
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Current revision

Crystal Structure of highly thermostable glycerol kinase from a hyperthermophilic archaeon

PDB ID 2zf5

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