1v1a

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:36, 1 May 2024) (edit) (undo)
 
(14 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1v1a.gif|left|200px]]
 
-
{{Structure
+
==2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS WITH BOUND 2-KETO-3-DEOXYGLUCONATE AND ADP==
-
|PDB= 1v1a |SIZE=350|CAPTION= <scene name='initialview01'>1v1a</scene>, resolution 2.10&Aring;
+
<StructureSection load='1v1a' size='340' side='right'caption='[[1v1a]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
-
|SITE= <scene name='pdbsite=AC1:Adp+Binding+Site+For+Chain+B'>AC1</scene>
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=KDG:2-KETO-3-DEOXYGLUCONATE'>KDG</scene> and <scene name='pdbligand=ADP:ADENOSINE-5&#39;-DIPHOSPHATE'>ADP</scene>
+
<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>
-
|ACTIVITY=
+
</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>
-
|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>, <scene name='pdbligand=KDG:2-KETO-3-DEOXYGLUCONATE'>KDG</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=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>
-
 
+
</table>
-
'''2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS WITH BOUND 2-KETO-3-DEOXYGLUCONATE AND ADP'''
+
== 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 ==
-
==Overview==
+
[[Image:Consurf_key_small.gif|200px|right]]
-
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.
+
Check<jmol>
-
 
+
<jmolCheckbox>
-
==About this Structure==
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/v1/1v1a_consurf.spt"</scriptWhenChecked>
-
1V1A is a [[Single protein]] structure of 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=1V1A OCA].
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
 
+
<text>to colour the structure by Evolutionary Conservation</text>
-
==Reference==
+
</jmolCheckbox>
-
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://www.ncbi.nlm.nih.gov/pubmed/15210349 15210349]
+
</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: Single protein]]
+
<div style="clear:both"></div>
-
[[Category: Thermus thermophilus]]
+
== References ==
-
[[Category: Inagaki, E.]]
+
<references/>
-
[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+
__TOC__
-
[[Category: Tahirov, T H.]]
+
</StructureSection>
-
[[Category: ADP]]
+
[[Category: Large Structures]]
-
[[Category: KDG]]
+
[[Category: Thermus thermophilus HB8]]
-
[[Category: 2-keto-3-deoxygluconate kinase]]
+
[[Category: Inagaki E]]
-
[[Category: atp]]
+
[[Category: Tahirov TH]]
-
[[Category: riken structural genomics/proteomics initiative]]
+
-
[[Category: rsgi]]
+
-
[[Category: structural genomic]]
+
-
[[Category: thermus thermophilus]]
+
-
[[Category: transferase]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 23 13:56:37 2008''
+

Current revision

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

PDB ID 1v1a

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1v1a"
Personal tools