1ua4: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(13 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1ua4.gif|left|200px]]


{{Structure
==Crystal Structure of an ADP-dependent Glucokinase from Pyrococcus furiosus==
|PDB= 1ua4 |SIZE=350|CAPTION= <scene name='initialview01'>1ua4</scene>, resolution 1.90&Aring;
<StructureSection load='1ua4' size='340' side='right'caption='[[1ua4]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=GLC:GLUCOSE'>GLC</scene> and <scene name='pdbligand=AMP:ADENOSINE MONOPHOSPHATE'>AMP</scene>
<table><tr><td colspan='2'>[[1ua4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UA4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UA4 FirstGlance]. <br>
|ACTIVITY= [http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2]  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
|GENE=  
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</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=1ua4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ua4 OCA], [https://pdbe.org/1ua4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ua4 RCSB], [https://www.ebi.ac.uk/pdbsum/1ua4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ua4 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/GLKA_PYRFU GLKA_PYRFU] 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> <ref>PMID:8530474</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/ua/1ua4_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=1ua4 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
ADP-dependent kinases are used in the modified Embden-Meyerhoff pathway of certain archaea. Our previous study has revealed a mechanism for ADP-dependent phosphoryl transfer by Thermococcus litoralis glucokinase (tlGK), and its evolutionary relationship with ATP-dependent ribokinases and adenosine kinases (PFKB carbohydrate kinase family members). Here, we report the crystal structure of glucokinase from Pyrococcus furiosus (pfGK) in a closed conformation complexed with glucose and AMP at 1.9A resolution. In comparison with the tlGK structure, the pfGK structure shows significant conformational changes in the small domain and a region around the hinge, suggesting glucose-induced domain closing. A part of the large domain next to the hinge is also shifted accompanied with domain closing. In the pfGK structure, glucose binds in a groove between the large and small domains, and the electron density of O1 atoms for both the alpha and beta-anomer configurations was observed. The structural details of the sugar-binding site of ADP-dependent glucokinase were firstly clarified and then site-directed mutagenesis analysis clarified the catalytic residues for ADP-dependent kinase, such as Arg205 and Asp451 of tlGK. Homology search and multiple alignment of amino acid sequences using the information obtained from the structures reveals that eucaryotic hypothetical proteins homologous to ADP-dependent kinases retain the residues for the recognition of a glucose substrate.


'''Crystal Structure of an ADP-dependent Glucokinase from Pyrococcus furiosus'''
Crystal structure of an ADP-dependent glucokinase from Pyrococcus furiosus: implications for a sugar-induced conformational change in ADP-dependent kinase.,Ito S, Fushinobu S, Jeong JJ, Yoshioka I, Koga S, Shoun H, Wakagi T J Mol Biol. 2003 Aug 22;331(4):871-83. PMID:12909015<ref>PMID:12909015</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1ua4" style="background-color:#fffaf0;"></div>


==Overview==
==See Also==
ADP-dependent kinases are used in the modified Embden-Meyerhoff pathway of certain archaea. Our previous study has revealed a mechanism for ADP-dependent phosphoryl transfer by Thermococcus litoralis glucokinase (tlGK), and its evolutionary relationship with ATP-dependent ribokinases and adenosine kinases (PFKB carbohydrate kinase family members). Here, we report the crystal structure of glucokinase from Pyrococcus furiosus (pfGK) in a closed conformation complexed with glucose and AMP at 1.9A resolution. In comparison with the tlGK structure, the pfGK structure shows significant conformational changes in the small domain and a region around the hinge, suggesting glucose-induced domain closing. A part of the large domain next to the hinge is also shifted accompanied with domain closing. In the pfGK structure, glucose binds in a groove between the large and small domains, and the electron density of O1 atoms for both the alpha and beta-anomer configurations was observed. The structural details of the sugar-binding site of ADP-dependent glucokinase were firstly clarified and then site-directed mutagenesis analysis clarified the catalytic residues for ADP-dependent kinase, such as Arg205 and Asp451 of tlGK. Homology search and multiple alignment of amino acid sequences using the information obtained from the structures reveals that eucaryotic hypothetical proteins homologous to ADP-dependent kinases retain the residues for the recognition of a glucose substrate.
*[[Hexokinase 3D structures|Hexokinase 3D structures]]
 
== References ==
==About this Structure==
<references/>
1UA4 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UA4 OCA].
__TOC__
 
</StructureSection>
==Reference==
[[Category: Large Structures]]
Crystal structure of an ADP-dependent glucokinase from Pyrococcus furiosus: implications for a sugar-induced conformational change in ADP-dependent kinase., Ito S, Fushinobu S, Jeong JJ, Yoshioka I, Koga S, Shoun H, Wakagi T, J Mol Biol. 2003 Aug 22;331(4):871-83. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12909015 12909015]
[[Category: Glucokinase]]
[[Category: Pyrococcus furiosus]]
[[Category: Pyrococcus furiosus]]
[[Category: Single protein]]
[[Category: Fushinobu S]]
[[Category: Fushinobu, S.]]
[[Category: Ito S]]
[[Category: Ito, S.]]
[[Category: Jeong JJ]]
[[Category: Jeong, J J.]]
[[Category: Koga S]]
[[Category: Koga, S.]]
[[Category: Shoun H]]
[[Category: Shoun, H.]]
[[Category: Wakagi T]]
[[Category: Wakagi, T.]]
[[Category: Yoshioka I]]
[[Category: Yoshioka, I.]]
[[Category: AMP]]
[[Category: GLC]]
[[Category: kinase]]
[[Category: transferase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 14:29:19 2008''

Latest revision as of 02:49, 28 December 2023

Crystal Structure of an ADP-dependent Glucokinase from Pyrococcus furiosusCrystal Structure of an ADP-dependent Glucokinase from Pyrococcus furiosus

Structural highlights

1ua4 is a 1 chain structure with sequence from Pyrococcus furiosus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.9Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GLKA_PYRFU 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] [2]

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

ADP-dependent kinases are used in the modified Embden-Meyerhoff pathway of certain archaea. Our previous study has revealed a mechanism for ADP-dependent phosphoryl transfer by Thermococcus litoralis glucokinase (tlGK), and its evolutionary relationship with ATP-dependent ribokinases and adenosine kinases (PFKB carbohydrate kinase family members). Here, we report the crystal structure of glucokinase from Pyrococcus furiosus (pfGK) in a closed conformation complexed with glucose and AMP at 1.9A resolution. In comparison with the tlGK structure, the pfGK structure shows significant conformational changes in the small domain and a region around the hinge, suggesting glucose-induced domain closing. A part of the large domain next to the hinge is also shifted accompanied with domain closing. In the pfGK structure, glucose binds in a groove between the large and small domains, and the electron density of O1 atoms for both the alpha and beta-anomer configurations was observed. The structural details of the sugar-binding site of ADP-dependent glucokinase were firstly clarified and then site-directed mutagenesis analysis clarified the catalytic residues for ADP-dependent kinase, such as Arg205 and Asp451 of tlGK. Homology search and multiple alignment of amino acid sequences using the information obtained from the structures reveals that eucaryotic hypothetical proteins homologous to ADP-dependent kinases retain the residues for the recognition of a glucose substrate.

Crystal structure of an ADP-dependent glucokinase from Pyrococcus furiosus: implications for a sugar-induced conformational change in ADP-dependent kinase.,Ito S, Fushinobu S, Jeong JJ, Yoshioka I, Koga S, Shoun H, Wakagi T J Mol Biol. 2003 Aug 22;331(4):871-83. PMID:12909015[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ 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
  2. ↑ Kengen SW, Tuininga JE, de Bok FA, Stams AJ, de Vos WM. Purification and characterization of a novel ADP-dependent glucokinase from the hyperthermophilic archaeon Pyrococcus furiosus. J Biol Chem. 1995 Dec 22;270(51):30453-7. PMID:8530474
  3. ↑ Ito S, Fushinobu S, Jeong JJ, Yoshioka I, Koga S, Shoun H, Wakagi T. Crystal structure of an ADP-dependent glucokinase from Pyrococcus furiosus: implications for a sugar-induced conformational change in ADP-dependent kinase. J Mol Biol. 2003 Aug 22;331(4):871-83. PMID:12909015

1ua4, resolution 1.90Å

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=1ua4&oldid=4006723"