|
|
| Line 3: |
Line 3: |
| | <StructureSection load='2zf5' size='340' side='right'caption='[[2zf5]], [[Resolution|resolution]] 2.40Å' scene=''> | | <StructureSection load='2zf5' size='340' side='right'caption='[[2zf5]], [[Resolution|resolution]] 2.40Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2zf5]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_kodakaraensis_(strain_kod1) Pyrococcus kodakaraensis (strain 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 [http://proteopedia.org/fgij/fg.htm?mol=2ZF5 FirstGlance]. <br> | + | <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> |
| - | </td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycerol_kinase Glycerol kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.30 2.7.1.30] </span></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]] 2.4Å</td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2zf5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zf5 OCA], [http://pdbe.org/2zf5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zf5 RCSB], [http://www.ebi.ac.uk/pdbsum/2zf5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2zf5 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=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> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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> | + | [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 == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| Line 35: |
Line 35: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Glycerol kinase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Kanaya, S]] | + | [[Category: Thermococcus kodakarensis KOD1]] |
| - | [[Category: Katsumi, R]] | + | [[Category: Kanaya S]] |
| - | [[Category: Koga, Y]] | + | [[Category: Katsumi R]] |
| - | [[Category: Matsumura, H]] | + | [[Category: Koga Y]] |
| - | [[Category: Takano, K]] | + | [[Category: Matsumura H]] |
| - | [[Category: You, D J]] | + | [[Category: Takano K]] |
| - | [[Category: Atp-binding]]
| + | [[Category: You D-J]] |
| - | [[Category: Glycerol metabolism]]
| + | |
| - | [[Category: Hyperthermophilic archaeon]]
| + | |
| - | [[Category: Nucleotide-binding]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
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][1]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
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 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[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Koga Y, Morikawa M, Haruki M, Nakamura H, Imanaka T, Kanaya S. Thermostable glycerol kinase from a hyperthermophilic archaeon: gene cloning and characterization of the recombinant enzyme. Protein Eng. 1998 Dec;11(12):1219-27. PMID:9930671
- ↑ Koga Y, Katsumi R, You DJ, Matsumura H, Takano K, Kanaya S. Crystal structure of highly thermostable glycerol kinase from a hyperthermophilic archaeon in a dimeric form. FEBS J. 2008 May;275(10):2632-43. Epub 2008 Apr 17. PMID:18422647 doi:10.1111/j.1742-4658.2008.06410.x
|
