2var: Difference between revisions

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<StructureSection load='2var' size='340' side='right'caption='[[2var]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
<StructureSection load='2var' size='340' side='right'caption='[[2var]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2var]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/'saccharolobus_solfataricus' 'saccharolobus solfataricus']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VAR OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2VAR FirstGlance]. <br>
<table><tr><td colspan='2'>[[2var]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_35091 Atcc 35091]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VAR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VAR FirstGlance]. <br>
</td></tr><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=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=KDF:3-DEOXY-ALPHA-D-ERYTHRO-HEX-2-ULOFURANOSONIC+ACID'>KDF</scene>, <scene name='pdbligand=KDG:2-KETO-3-DEOXYGLUCONATE'>KDG</scene></td></tr>
</td></tr><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=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=KDF:3-DEOXY-ALPHA-D-ERYTHRO-HEX-2-ULOFURANOSONIC+ACID'>KDF</scene>, <scene name='pdbligand=KDG:2-KETO-3-DEOXYGLUCONATE'>KDG</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2v78|2v78]]</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2v78|2v78]]</div></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Fructokinase Fructokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.4 2.7.1.4] </span></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Fructokinase Fructokinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.4 2.7.1.4] </span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2var FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2var OCA], [http://pdbe.org/2var PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2var RCSB], [http://www.ebi.ac.uk/pdbsum/2var PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2var ProSAT]</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=2var FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2var OCA], [https://pdbe.org/2var PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2var RCSB], [https://www.ebi.ac.uk/pdbsum/2var PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2var ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/KDGK_SULSO KDGK_SULSO]] Involved in the degradation of glucose and galactose via the semi-phosphorylative Entner-Doudoroff pathway. Catalyzes the phosphorylation of 2-keto-3-deoxygluconate (KDG) and 2-keto-3-deoxygalactonate (KDGal) to produce 2-keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-3-deoxy-6-phosphogalactonate (KDPGal), respectively.<ref>PMID:15869466</ref> <ref>PMID:16330030</ref> <ref>PMID:16794308</ref>   
[[https://www.uniprot.org/uniprot/KDGK_SULSO KDGK_SULSO]] Involved in the degradation of glucose and galactose via the semi-phosphorylative Entner-Doudoroff pathway. Catalyzes the phosphorylation of 2-keto-3-deoxygluconate (KDG) and 2-keto-3-deoxygalactonate (KDGal) to produce 2-keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-3-deoxy-6-phosphogalactonate (KDPGal), respectively.<ref>PMID:15869466</ref> <ref>PMID:16330030</ref> <ref>PMID:16794308</ref>   
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Saccharolobus solfataricus]]
[[Category: Atcc 35091]]
[[Category: Fructokinase]]
[[Category: Fructokinase]]
[[Category: Large Structures]]
[[Category: Large Structures]]

Revision as of 15:43, 23 March 2022

Crystal structure of Sulfolobus solfataricus 2-keto-3-deoxygluconate kinase complexed with 2-keto-3-deoxygluconateCrystal structure of Sulfolobus solfataricus 2-keto-3-deoxygluconate kinase complexed with 2-keto-3-deoxygluconate

Structural highlights

2var is a 3 chain structure with sequence from Atcc 35091. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:, , ,
Activity:Fructokinase, with EC number 2.7.1.4
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[KDGK_SULSO] Involved in the degradation of glucose and galactose via the semi-phosphorylative Entner-Doudoroff pathway. Catalyzes the phosphorylation of 2-keto-3-deoxygluconate (KDG) and 2-keto-3-deoxygalactonate (KDGal) to produce 2-keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-3-deoxy-6-phosphogalactonate (KDPGal), respectively.[1] [2] [3]

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

The hyperthermophilic archaeon Sulfolobus solfataricus grows optimally above 353 K and utilizes an unusual promiscuous nonphosphorylative Entner-Doudoroff pathway to metabolize both glucose and galactose. It has been proposed that a part-phosphorylative Entner-Doudoroff pathway occurs in parallel in S. solfataricus, in which the 2-keto-3-deoxygluconate kinase (KDGK) is promiscuous for both glucose and galactose metabolism. Recombinant S. solfataricus KDGK protein was expressed in Escherichia coli, purified and crystallized in 0.1 M sodium acetate pH 4.1 and 1.4 M NaCl. The crystal structure of apo S. solfataricus KDGK was solved by molecular replacement to a resolution of 2.0 A and a ternary complex with 2-keto-3-deoxygluconate (KDGlu) and an ATP analogue was resolved at 2.1 A. The complex suggests that the structural basis for the enzyme's ability to phosphorylate KDGlu and 2-keto-3-deoxygalactonate (KDGal) is derived from a subtle repositioning of residues that are conserved in homologous nonpromiscuous kinases.

The structure of Sulfolobus solfataricus 2-keto-3-deoxygluconate kinase.,Potter JA, Kerou M, Lamble HJ, Bull SD, Hough DW, Danson MJ, Taylor GL Acta Crystallogr D Biol Crystallogr. 2008 Dec;64(Pt 12):1283-7. Epub 2008, Nov 18. PMID:19018105[4]

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

See Also

References

  1. ↑ Ahmed H, Ettema TJ, Tjaden B, Geerling AC, van der Oost J, Siebers B. The semi-phosphorylative Entner-Doudoroff pathway in hyperthermophilic archaea: a re-evaluation. Biochem J. 2005 Sep 1;390(Pt 2):529-40. PMID:15869466 doi:http://dx.doi.org/10.1042/BJ20041711
  2. ↑ Lamble HJ, Theodossis A, Milburn CC, Taylor GL, Bull SD, Hough DW, Danson MJ. Promiscuity in the part-phosphorylative Entner-Doudoroff pathway of the archaeon Sulfolobus solfataricus. FEBS Lett. 2005 Dec 19;579(30):6865-9. Epub 2005 Dec 1. PMID:16330030 doi:http://dx.doi.org/10.1016/j.febslet.2005.11.028
  3. ↑ Kim S, Lee SB. Characterization of Sulfolobus solfataricus 2-keto-3-deoxy-D-gluconate kinase in the modified Entner-Doudoroff pathway. Biosci Biotechnol Biochem. 2006 Jun;70(6):1308-16. PMID:16794308 doi:http://dx.doi.org/10.1271/bbb.50566
  4. ↑ Potter JA, Kerou M, Lamble HJ, Bull SD, Hough DW, Danson MJ, Taylor GL. The structure of Sulfolobus solfataricus 2-keto-3-deoxygluconate kinase. Acta Crystallogr D Biol Crystallogr. 2008 Dec;64(Pt 12):1283-7. Epub 2008, Nov 18. PMID:19018105 doi:10.1107/S0907444908036111

2var, resolution 2.10Å

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