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1v1b

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2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS WITH BOUND ATP

Structural highlights

1v1b is a 4 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 2.6Å
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

↑ 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
↑ 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

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1v1b"

Categories: Large Structures | Thermus thermophilus HB8 | Inagaki E | Tahirov TH

@@ Line 1: / Line 1: @@
 ==2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS WITH BOUND ATP==
-<StructureSection load='1v1b' size='340' side='right' caption='[[1v1b]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+<StructureSection load='1v1b' size='340' side='right'caption='[[1v1b]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1v1b]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V1B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1V1B FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1v1b]] is a 4 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=1V1B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V1B FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1j5v|1j5v]], [[1v19|1v19]], [[1v1a|1v1a]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1v1b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v1b OCA], [http://pdbe.org/1v1b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1v1b RCSB], [http://www.ebi.ac.uk/pdbsum/1v1b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1v1b ProSAT], [http://www.topsan.org/Proteins/RSGI/1v1b TOPSAN]</span></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=1v1b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v1b OCA], [https://pdbe.org/1v1b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v1b RCSB], [https://www.ebi.ac.uk/pdbsum/1v1b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v1b ProSAT], [https://www.topsan.org/Proteins/RSGI/1v1b 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]]
@@ Line 31: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Thet8]]
+[[Category: Large Structures]]
-[[Category: Inagaki, E]]
+[[Category: Thermus thermophilus HB8]]
-[[Category: Tahirov, T H]]
+[[Category: Inagaki E]]
-[[Category: 2-keto-3-deoxygluconate kinase]]
+[[Category: Tahirov TH]]
-[[Category: Atp]]
-[[Category: Structural genomic]]
-[[Category: Rsgi]]
-[[Category: Thermus thermophilus]]
-[[Category: Transferase]]

1v1b

From Proteopedia

Current revision

2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS WITH BOUND ATP

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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