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| - | [[Image:1gc5.jpg|left|200px]] | |
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| - | {{Structure
| + | ==CRYSTAL STRUCTURE OF A NOVEL ADP-DEPENDENT GLUCOKINASE FROM THERMOCOCCUS LITORALIS== |
| - | |PDB= 1gc5 |SIZE=350|CAPTION= <scene name='initialview01'>1gc5</scene>, resolution 2.3Å
| + | <StructureSection load='1gc5' size='340' side='right'caption='[[1gc5]], [[Resolution|resolution]] 2.30Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=ADP:ADENOSINE-5'-DIPHOSPHATE'>ADP</scene> | + | <table><tr><td colspan='2'>[[1gc5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_litoralis Thermococcus litoralis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GC5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GC5 FirstGlance]. <br> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/ADP-specific_glucokinase ADP-specific glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.147 2.7.1.147]
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3Å</td></tr> |
| - | |GENE= | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></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=1gc5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gc5 OCA], [https://pdbe.org/1gc5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gc5 RCSB], [https://www.ebi.ac.uk/pdbsum/1gc5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gc5 ProSAT]</span></td></tr> |
| | + | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/GLKA_THELN GLKA_THELN] Catalyzes the phosphorylation of D-glucose to D-glucose 6-phosphate using ADP as the phosphate donor. Can also use CDP as the phosphoryl group donor and D-glucosamine and D-1,5-anhydroglucitol as the phosphoryl group acceptor.<ref>PMID:11098152</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/gc/1gc5_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=1gc5 ConSurf]. |
| | + | <div style="clear:both"></div> |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | BACKGROUND: ATP is the most common phosphoryl group donor for kinases. However, certain hyperthermophilic archaea such as Thermococcus litoralis and Pyrococcus furiosus utilize unusual ADP-dependent glucokinases and phosphofructokinases in their glycolytic pathways. These ADP-dependent kinases are homologous to each other but show no sequence similarity to any of the hitherto known ATP-dependent enzymes. RESULTS: We solved the crystal structure at 2.3 A resolution of an ADP-dependent glucokinase from T. litoralis (tlGK) complexed with ADP. The overall structure can be divided into large and small alpha/beta domains, and the ADP molecule is buried in a shallow pocket in the large domain. Unexpectedly, the structure was similar to those of two ATP-dependent kinases, ribokinase and adenosine kinase. Comparison based on three-dimensional structure revealed that several motifs important both in structure and function are conserved, and the recognition of the alpha- and beta-phosphate of the ADP in the tlGK was almost identical with the recognition of the beta- and gamma-phosphate of ATP in these ATP-dependent kinases. CONCLUSIONS: Noticeable points of our study are the first structure of ADP-dependent kinase, the structural similarity to members of the ATP-dependent ribokinase family, its rare nucleotide specificity caused by a shift in nucleotide binding position by one phosphate unit, and identification of the residues that discriminate ADP- and ATP-dependence. The strict conservation of the binding site for the terminal and adjacent phosphate moieties suggests a common ancestral origin of both the ATP- and ADP-dependent kinases. |
| | | | |
| - | '''CRYSTAL STRUCTURE OF A NOVEL ADP-DEPENDENT GLUCOKINASE FROM THERMOCOCCUS LITORALIS'''
| + | Structural basis for the ADP-specificity of a novel glucokinase from a hyperthermophilic archaeon.,Ito S, Fushinobu S, Yoshioka I, Koga S, Matsuzawa H, Wakagi T Structure. 2001 Mar 7;9(3):205-14. PMID:11286887<ref>PMID:11286887</ref> |
| | | | |
| | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | + | </div> |
| | + | <div class="pdbe-citations 1gc5" style="background-color:#fffaf0;"></div> |
| | | | |
| - | ==Overview== | + | ==See Also== |
| - | BACKGROUND: ATP is the most common phosphoryl group donor for kinases. However, certain hyperthermophilic archaea such as Thermococcus litoralis and Pyrococcus furiosus utilize unusual ADP-dependent glucokinases and phosphofructokinases in their glycolytic pathways. These ADP-dependent kinases are homologous to each other but show no sequence similarity to any of the hitherto known ATP-dependent enzymes. RESULTS: We solved the crystal structure at 2.3 A resolution of an ADP-dependent glucokinase from T. litoralis (tlGK) complexed with ADP. The overall structure can be divided into large and small alpha/beta domains, and the ADP molecule is buried in a shallow pocket in the large domain. Unexpectedly, the structure was similar to those of two ATP-dependent kinases, ribokinase and adenosine kinase. Comparison based on three-dimensional structure revealed that several motifs important both in structure and function are conserved, and the recognition of the alpha- and beta-phosphate of the ADP in the tlGK was almost identical with the recognition of the beta- and gamma-phosphate of ATP in these ATP-dependent kinases. CONCLUSIONS: Noticeable points of our study are the first structure of ADP-dependent kinase, the structural similarity to members of the ATP-dependent ribokinase family, its rare nucleotide specificity caused by a shift in nucleotide binding position by one phosphate unit, and identification of the residues that discriminate ADP- and ATP-dependence. The strict conservation of the binding site for the terminal and adjacent phosphate moieties suggests a common ancestral origin of both the ATP- and ADP-dependent kinases.
| + | *[[Hexokinase 3D structures|Hexokinase 3D structures]] |
| - | | + | == References == |
| - | ==About this Structure==
| + | <references/> |
| - | 1GC5 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermococcus_litoralis Thermococcus litoralis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GC5 OCA].
| + | __TOC__ |
| - | | + | </StructureSection> |
| - | ==Reference== | + | [[Category: Large Structures]] |
| - | Structural basis for the ADP-specificity of a novel glucokinase from a hyperthermophilic archaeon., Ito S, Fushinobu S, Yoshioka I, Koga S, Matsuzawa H, Wakagi T, Structure. 2001 Mar 7;9(3):205-14. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11286887 11286887]
| + | |
| - | [[Category: ADP-specific glucokinase]]
| + | |
| - | [[Category: Single protein]] | + | |
| | [[Category: Thermococcus litoralis]] | | [[Category: Thermococcus litoralis]] |
| - | [[Category: Fushinobu, S.]] | + | [[Category: Fushinobu S]] |
| - | [[Category: Ito, S.]] | + | [[Category: Ito S]] |
| - | [[Category: Koga, S.]] | + | [[Category: Koga S]] |
| - | [[Category: Matsuzawa, H.]] | + | [[Category: Matsuzawa H]] |
| - | [[Category: Wakagi, T.]] | + | [[Category: Wakagi T]] |
| - | [[Category: Yoshioka, I.]] | + | [[Category: Yoshioka I]] |
| - | [[Category: ADP]]
| + | |
| - | [[Category: alfa/beta sandwich]]
| + | |
| - | [[Category: induced-fitting]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 11:21:11 2008''
| + | |
| Structural highlights
Function
GLKA_THELN Catalyzes the phosphorylation of D-glucose to D-glucose 6-phosphate using ADP as the phosphate donor. Can also use CDP as the phosphoryl group donor and D-glucosamine and D-1,5-anhydroglucitol as the phosphoryl group acceptor.[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
BACKGROUND: ATP is the most common phosphoryl group donor for kinases. However, certain hyperthermophilic archaea such as Thermococcus litoralis and Pyrococcus furiosus utilize unusual ADP-dependent glucokinases and phosphofructokinases in their glycolytic pathways. These ADP-dependent kinases are homologous to each other but show no sequence similarity to any of the hitherto known ATP-dependent enzymes. RESULTS: We solved the crystal structure at 2.3 A resolution of an ADP-dependent glucokinase from T. litoralis (tlGK) complexed with ADP. The overall structure can be divided into large and small alpha/beta domains, and the ADP molecule is buried in a shallow pocket in the large domain. Unexpectedly, the structure was similar to those of two ATP-dependent kinases, ribokinase and adenosine kinase. Comparison based on three-dimensional structure revealed that several motifs important both in structure and function are conserved, and the recognition of the alpha- and beta-phosphate of the ADP in the tlGK was almost identical with the recognition of the beta- and gamma-phosphate of ATP in these ATP-dependent kinases. CONCLUSIONS: Noticeable points of our study are the first structure of ADP-dependent kinase, the structural similarity to members of the ATP-dependent ribokinase family, its rare nucleotide specificity caused by a shift in nucleotide binding position by one phosphate unit, and identification of the residues that discriminate ADP- and ATP-dependence. The strict conservation of the binding site for the terminal and adjacent phosphate moieties suggests a common ancestral origin of both the ATP- and ADP-dependent kinases.
Structural basis for the ADP-specificity of a novel glucokinase from a hyperthermophilic archaeon.,Ito S, Fushinobu S, Yoshioka I, Koga S, Matsuzawa H, Wakagi T Structure. 2001 Mar 7;9(3):205-14. PMID:11286887[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Koga S, Yoshioka I, Sakuraba H, Takahashi M, Sakasegawa S, Shimizu S, Ohshima T. Biochemical characterization, cloning, and sequencing of ADP-dependent (AMP-forming) glucokinase from two hyperthermophilic archaea, Pyrococcus furiosus and Thermococcus litoralis. J Biochem. 2000 Dec;128(6):1079-85. PMID:11098152
- ↑ Ito S, Fushinobu S, Yoshioka I, Koga S, Matsuzawa H, Wakagi T. Structural basis for the ADP-specificity of a novel glucokinase from a hyperthermophilic archaeon. Structure. 2001 Mar 7;9(3):205-14. PMID:11286887
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