1v1a: Difference between revisions

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[[Image:1v1a.gif|left|200px]]<br />
<applet load="1v1a" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1v1a, resolution 2.10&Aring;" />
'''2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS WITH BOUND 2-KETO-3-DEOXYGLUCONATE AND ADP'''<br />


==Overview==
==2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS WITH BOUND 2-KETO-3-DEOXYGLUCONATE AND ADP==
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, ... [[http://ispc.weizmann.ac.il/pmbin/getpm?15210349 (full description)]]
<StructureSection load='1v1a' size='340' side='right'caption='[[1v1a]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[1v1a]] 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=1V1A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V1A FirstGlance]. <br>
1V1A is a [[http://en.wikipedia.org/wiki/Single_protein Single protein]] structure of sequence from [[http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]] with KDG and ADP as [[http://en.wikipedia.org/wiki/ligands ligands]]. Structure known Active Site: AC1. Full crystallographic information is available from [[http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1V1A OCA]].  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
 
<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>, <scene name='pdbligand=KDG:2-KETO-3-DEOXYGLUCONATE'>KDG</scene></td></tr>
==Reference==
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1v1a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v1a OCA], [https://pdbe.org/1v1a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v1a RCSB], [https://www.ebi.ac.uk/pdbsum/1v1a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v1a ProSAT], [https://www.topsan.org/Proteins/RSGI/1v1a TOPSAN]</span></td></tr>
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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15210349 15210349]
</table>
[[Category: Single protein]]
== Function ==
[[Category: Thermus thermophilus]]
[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>
[[Category: Inagaki, E.]]
== Evolutionary Conservation ==
[[Category: RSGI, RIKEN.Structural.Genomics/Proteomics.Initiative.]]
[[Image:Consurf_key_small.gif|200px|right]]
[[Category: Tahirov, T.H.]]
Check<jmol>
[[Category: ADP]]
  <jmolCheckbox>
[[Category: KDG]]
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/v1/1v1a_consurf.spt"</scriptWhenChecked>
[[Category: 2-keto-3-deoxygluconate kinase]]
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
[[Category: atp]]
    <text>to colour the structure by Evolutionary Conservation</text>
[[Category: riken structural genomics/proteomics initiative]]
  </jmolCheckbox>
[[Category: rsgi]]
</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=1v1a ConSurf].
[[Category: structural genomics]]
<div style="clear:both"></div>
[[Category: thermus thermophilus]]
== References ==
[[Category: transferase]]
<references/>
 
__TOC__
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Oct 30 12:36:28 2007''
</StructureSection>
[[Category: Large Structures]]
[[Category: Thermus thermophilus HB8]]
[[Category: Inagaki E]]
[[Category: Tahirov TH]]

Latest revision as of 09:36, 1 May 2024

2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS WITH BOUND 2-KETO-3-DEOXYGLUCONATE AND ADP2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS WITH BOUND 2-KETO-3-DEOXYGLUCONATE AND ADP

Structural highlights

1v1a 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 2.1Å
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.

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

1v1a, resolution 2.10Å

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