1v19: Difference between revisions

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==2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS==
The line below this paragraph, containing "STRUCTURE_1v19", creates the "Structure Box" on the page.
<StructureSection load='1v19' size='340' side='right'caption='[[1v19]], [[Resolution|resolution]] 2.30&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'>[[1v19]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V19 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V19 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]] 2.3&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene></td></tr>
{{STRUCTURE_1v19|  PDB=1v19  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1v19 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v19 OCA], [https://pdbe.org/1v19 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v19 RCSB], [https://www.ebi.ac.uk/pdbsum/1v19 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v19 ProSAT], [https://www.topsan.org/Proteins/RSGI/1v19 TOPSAN]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/KDGK_THET8 KDGK_THET8] Involved in the degradation of glucose via the semi-phosphorylative Entner-Doudoroff pathway. Catalyzes the phosphorylation of 2-keto-3-deoxygluconate (KDG) to produce 2-keto-3-deoxy-6-phosphogluconate (KDPG).<ref>PMID:15210349</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/v1/1v19_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=1v19 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
2-Keto-3-deoxygluconate kinase (KDGK) catalyzes the phosphorylation of 2-keto-3-deoxygluconate (KDG) to 2-keto-3-deoxy-6-phosphogluconate (KDGP). The genome sequence of Thermus thermophilus HB8 contains an open reading frame that has a 30% identity to Escherichia coli KDGK. The KDGK activity of T.thermophilus protein (TtKDGK) has been confirmed, and its crystal structure has been determined by the molecular replacement method and refined with two crystal forms to 2.3 angstroms and 3.2 angstroms, respectively. The enzyme is a hexamer organized as a trimer of dimers. Each subunit is composed of two domains, a larger alpha/beta domain and a smaller beta-sheet domain, similar to that of ribokinase and adenosine kinase, members of the PfkB family of carbohydrate kinases. Furthermore, the TtKDGK structure with its KDG and ATP analogue was determined and refined at 2.1 angstroms. The bound KDG was observed predominantly as an open chain structure. The positioning of ligands and the conservation of important catalytic residues suggest that the reaction mechanism is likely to be similar to that of other members of the PfkB family, including ribokinase. In particular, the Asp251 is postulated to have a role in transferring the gamma-phosphate of ATP to the 5'-hydroxyl group of KDG.


===2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS===
Structure of Thermus thermophilus 2-Keto-3-deoxygluconate kinase: evidence for recognition of an open chain substrate.,Ohshima N, Inagaki E, Yasuike K, Takio K, Tahirov TH J Mol Biol. 2004 Jul 9;340(3):477-89. PMID:15210349<ref>PMID:15210349</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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The line below this paragraph, {{ABSTRACT_PUBMED_15210349}}, adds the Publication Abstract to the page
<div class="pdbe-citations 1v19" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 15210349 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_15210349}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
[[1v19]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V19 OCA].
[[Category: Thermus thermophilus HB8]]
 
[[Category: Inagaki E]]
==Reference==
[[Category: Tahirov TH]]
<ref group="xtra">PMID:15210349</ref><ref group="xtra">PMID:15039578</ref><references group="xtra"/>
[[Category: Thermus thermophilus]]
[[Category: Inagaki, E.]]
[[Category: Tahirov, T H.]]
[[Category: 2-keto-3-deoxygluconate kinase]]
[[Category: Riken structural genomics/proteomics initiative]]
[[Category: Rsgi]]
[[Category: Structural genomic]]
[[Category: Thermus thermophilus]]
[[Category: Transferase]]

Latest revision as of 16:07, 13 December 2023

2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS

Structural highlights

1v19 is a 2 chain structure with sequence from Thermus thermophilus HB8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.3Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

KDGK_THET8 Involved in the degradation of glucose via the semi-phosphorylative Entner-Doudoroff pathway. Catalyzes the phosphorylation of 2-keto-3-deoxygluconate (KDG) to produce 2-keto-3-deoxy-6-phosphogluconate (KDPG).[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

2-Keto-3-deoxygluconate kinase (KDGK) catalyzes the phosphorylation of 2-keto-3-deoxygluconate (KDG) to 2-keto-3-deoxy-6-phosphogluconate (KDGP). The genome sequence of Thermus thermophilus HB8 contains an open reading frame that has a 30% identity to Escherichia coli KDGK. The KDGK activity of T.thermophilus protein (TtKDGK) has been confirmed, and its crystal structure has been determined by the molecular replacement method and refined with two crystal forms to 2.3 angstroms and 3.2 angstroms, respectively. The enzyme is a hexamer organized as a trimer of dimers. Each subunit is composed of two domains, a larger alpha/beta domain and a smaller beta-sheet domain, similar to that of ribokinase and adenosine kinase, members of the PfkB family of carbohydrate kinases. Furthermore, the TtKDGK structure with its KDG and ATP analogue was determined and refined at 2.1 angstroms. The bound KDG was observed predominantly as an open chain structure. The positioning of ligands and the conservation of important catalytic residues suggest that the reaction mechanism is likely to be similar to that of other members of the PfkB family, including ribokinase. In particular, the Asp251 is postulated to have a role in transferring the gamma-phosphate of ATP to the 5'-hydroxyl group of KDG.

Structure of Thermus thermophilus 2-Keto-3-deoxygluconate kinase: evidence for recognition of an open chain substrate.,Ohshima N, Inagaki E, Yasuike K, Takio K, Tahirov TH J Mol Biol. 2004 Jul 9;340(3):477-89. PMID:15210349[2]

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

References

  1. ↑ Ohshima N, Inagaki E, Yasuike K, Takio K, Tahirov TH. Structure of Thermus thermophilus 2-Keto-3-deoxygluconate kinase: evidence for recognition of an open chain substrate. J Mol Biol. 2004 Jul 9;340(3):477-89. PMID:15210349 doi:http://dx.doi.org/10.1016/j.jmb.2004.04.074
  2. ↑ Ohshima N, Inagaki E, Yasuike K, Takio K, Tahirov TH. Structure of Thermus thermophilus 2-Keto-3-deoxygluconate kinase: evidence for recognition of an open chain substrate. J Mol Biol. 2004 Jul 9;340(3):477-89. PMID:15210349 doi:http://dx.doi.org/10.1016/j.jmb.2004.04.074

1v19, resolution 2.30Å

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