Kdo-8-phosphate synthase

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{{STRUCTURE_3fyp| PDB=3fyp | SIZE=400| SCENE= |right|CAPTION=Kdo-8-phosphate synthase tetramer complex with phosphoenolpyruvate, glycerol, Cl- (green), Na+(large purple) and Mn+2 (small purple) ion, [[3fyp]] }}
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<StructureSection load='' size='350' side='right' scene='52/525184/Cv/2' caption='Metallo Kdo-8-phosphate synthase tetramer complex with phosphoenolpyruvate, glycerol, Cl- (green), Na+ (large purple) and Mn+2 (small purple) ion, [[3fyp]]'>
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'''Kdo-8-phosphate synthase''' (KPS) catalyzes the formation of the phosphorylated rare sugar Kdo-8-phosphate (Kdo-8-P) from phosphoenolpyruvate (PEP) and D-arabinose-5-phosphate (A5P). KPS is a metal-requiring enzyme.
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== Function ==
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Kdo-8-P is found in cell walls of higher plants and some green algae.
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'''Kdo-8-phosphate synthase''' or '''2-dehydro-3-deoxyphosphooctonate aldolase''' (KPS) catalyzes the formation of the phosphorylated rare sugar Kdo-8-phosphate (Kdo-8-P) from phosphoenolpyruvate (PEP) and D-arabinose-5-phosphate (A5P). Some bacteria like ''Aquifex aeolicus'' have '''Metallo KPS''' which is a metal-requiring enzyme while others like ''E.coli'' have a '''Non-metallo KPS''' which does not require a divalent cation for its activity. Kdo-8-P is found in cell walls of higher plants and some green algae<ref>PMID:11904225</ref>.
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== Structural highlights ==
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The biological assembly of Metallo Kdo-8-phosphate synthase from ''Neisseria meningitidis'' is <scene name='52/525184/Cv/7'>homotetramer</scene>. The <scene name='52/525184/Cv/8'>active site of the metallo KPS contains a divalent cation and the PEP substrate</scene><ref>PMID:19447118</ref>. Water molecules shown as red spheres.
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</StructureSection>
==3D structures of Kdo-8-phosphate synthase==
==3D structures of Kdo-8-phosphate synthase==
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Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
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{{#tree:id=OrganizedByTopic|openlevels=0|
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===Metallo Kdo8P===
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*Metallo Kdo8P
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[[1fxp]] - AaKPS + Cd – Aquifex aeolicus<br />
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**[[1fxp]] - AaKPS + Cd – ''Aquifex aeolicus''<br />
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[[1lrn]], [[1t99]] - AaKPS (mutant) + Cd<br />
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**[[1lrn]], [[1t99]] - AaKPS (mutant) + Cd<br />
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[[2qkf]] – NmKPS + Na – Neisseria meningitides<br />
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**[[1fx6]] - AaKPS <br />
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[[3fyo]] - NmKPS (mutant) + Mn<br />
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**[[2nws]], [[2nx3]] - AaKPS (mutant) <br />
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[[3qpy]], [[3qpz]], [[3qq0]], [[3stc]], [[3ste]], [[3stf]] - NmKPS (mutant) + Na
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**[[2qkf]] – NmKPS + Na – ''Neisseria meningitides''<br />
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**[[3fyo]] - NmKPS (mutant) + Mn<br />
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**[[3qpy]], [[3qpz]], [[3qq0]], [[3stc]], [[3ste]], [[3stf]], [[4jte]], [[4jtf]], [[4jtg]], [[4jth]], [[4jti]], [[4jtj]], [[4jtk]], [[4jtl]] - NmKPS (mutant) + Na<br />
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**[[3qq1]], [[3stg]] - NmKPS (mutant) <br />
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**[[3sz8]] – BpKPS-2 – ''Burkholderia pseudomallei''<br />
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**[[4lu0]] – KPS – ''Pseudomonas aeruginosa''<br />
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**[[4z1a]] – HpKPS – ''Helicobacter pylori''<br />
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**[[4z1b]] - HpKPS (mutant)<br />
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**[[4z1c]] - HpKPS + Cd<br />
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**[[6bng]] – KPS – ''Acinetobacter baumannii''<br />
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==Metallo Kdo8P binary complex==
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*''Metallo Kdo8P binary complex''
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[[1fws]] – AaKPS + PEP + Cd<br />
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**[[1fws]] – AaKPS + PEP + Cd<br />
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[[3e0i]] - AaKPS + PEP + Cu<br />
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**[[3e0i]] - AaKPS + PEP + Cu<br />
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[[1lro]], [[1t96]] - AaKPS (mutant) + PEP + Cd<br />
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**[[1lro]], [[1t96]] - AaKPS (mutant) + PEP + Cd<br />
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[[1pck]] - AaKPS + PEP derivative + Cd<br />
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**[[1pck]] - AaKPS + PEP derivative + Cd<br />
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[[1pe1]] - AaKPS + phosphoglyceric acid + Cd<br />
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**[[1pe1]] - AaKPS + phosphoglyceric acid + Cd<br />
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[[2a21]] - EcKPS + PEP + Zn - Escherichia coli<br />
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**[[2a21]] - AaKPS + PEP + Zn <br />
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[[1jcx]], [[1pcw]] - AaKPS + inhibitor + Cd<br />
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**[[1jcx]], [[1pcw]] - AaKPS + inhibitor + Cd<br />
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[[1fy6]] - AaKPS + A5P + Cd<br />
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**[[1fy6]] - AaKPS + A5P + Cd<br />
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[[3e12]] - AaKPS + Kdo-8-P + Cu<br />
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**[[3e12]] - AaKPS + Kdo-8-P + Cu<br />
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[[3fyp]] - NmKPS (mutant) + PEP + Mn
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**[[2nxi]], [[1fwn]] - AaKPS + PEP<br />
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**[[2nwr]], [[2nxh]] - AaKPS (mutant) + PEP<br />
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**[[4z1d]] - HpKPS + PEP + Zn<br />
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**[[3fyp]] - NmKPS (mutant) + PEP + Mn<br />
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**[[3tmq]] - BpKPS + arabinose-5-phosphate<br />
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==Metallo Kdo8P ternary complex==
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*''Metallo Kdo8P ternary complex''
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[[1fwt]] - AaKPS + erythrose-4-phosphate + PEP + Cd<br />
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**[[1fwt]] - AaKPS + erythrose-4-phosphate + PEP + Cd<br />
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[[1jcy]] - AaKPS + ribose-5-phosphate + PEP + Cd<br />
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**[[1jcy]] - AaKPS + ribose-5-phosphate + PEP + Cd<br />
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[[1zha]] - AaKPS (mutant) + ribose-5-phosphate + PEP + Cd<br />
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**[[1zha]] - AaKPS (mutant) + ribose-5-phosphate + PEP + Cd<br />
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[[1zji]] - AaKPS (mutant) + ribose-5-phosphate + phosphoglyceric acid + Cd<br />
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**[[1zji]] - AaKPS (mutant) + ribose-5-phosphate + phosphoglyceric acid + Cd<br />
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[[1fww]] - AaKPS + A5P + PEP + Cd<br />
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**[[1fww]] - AaKPS + A5P + PEP + Cd<br />
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[[2a2i]] - AaKPS + A5P + PEP + Zn<br />
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**[[2a2i]] - AaKPS + A5P + PEP + Zn<br />
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[[1lrq]], [[1t8x]] - AaKPS (mutant) + A5P + PEP + Cd<br />
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**[[1lrq]], [[1t8x]] - AaKPS (mutant) + A5P + PEP + Cd<br />
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**[[1fxq]] - AaKPS + A5P + PEP<br />
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**[[2nx1]], [[2ef9]] - AaKPS (mutant) + A5P + PEP<br />
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**[[2nxg]] - AaKPS (mutant) + octanoic acid derivative + A5P + PEP<br />
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**[[3und]] - BpKPS + arabinose-5-phosphate + PEP<br />
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===Non-metallo Kdo8P===
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*Non-metallo Kdo8P
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[[1d9e]], [[1gg0]], [[1x8f]] – EcKPS <br />
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**[[1d9e]], [[1gg0]], [[1x8f]], [[6u57]] – EcKPS - ''Escherichia coli''<br />
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[[1fx6]] - AaKPS <br />
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**[[1o60]] - KPS – ''Haemophilus influenza''<br />
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[[2nws]] - AaKPS (mutant) <br />
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**[[3e9a]] - KPS – ''Vibrio cholerae''<br />
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[[1o60]] - KPS – Haemophilus influenza<br />
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**[[3fs2]] - KPS – ''Brucella melitensis''<br />
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[[3e9a]] - KPS – Vibrio cholera<br />
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**[[3t4c]], [[3tml]] - KPS – ''Burkholderia ambifaria''<br />
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[[3fs2]] - KPS – Brucella melitensis<br />
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**[[6mdy]] – KPS – ''Legionella pneumophila''<br />
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[[3qq1]], [[3stg]] - NmKPS (mutant) <br />
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[[3t4c]], [[3tml]] - KPS – Burkholderia ambifaria
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==Non-metallo Kdo8P binary complex==
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*''Non-metallo Kdo8P binary complex''
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[[2nxi]], [[1fwn]] - AaKPS + PEP<br />
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**[[1g7u]], [[1q3n]] - EcKPS + PEP<br />
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[[2nwr]], [[2nxh]] - AaKPS (mutant) + PEP<br />
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**[[1phq]], [[1pl9]] - EcKPS + PEP derivative<br />
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[[1g7u]], [[1q3n]] - EcKPS + PEP<br />
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**[[1phw]] - EcKPS + A5P derivative<br />
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[[1phq]], [[1pl9]] - EcKPS + PEP derivative<br />
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**[[1g7v]] - EcKPS + inhibitor<br />
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[[1phw]] - EcKPS + A5P derivative<br />
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**[[1x6u]] - EcKPS + Kdo-8-P
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[[1g7v]] - EcKPS + inhibitor<br />
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[[1x6u]] - EcKPS + Kdo-8-P
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==Non-metallo Kdo8P ternary complex==
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[[1fxq]] - AaKPS + A5P + PEP<br />
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[[2nx1]], [[2ef9]] - AaKPS (mutant) + A5P + PEP<br />
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[[2nxg]] - AaKPS (mutant) + octanoic acid derivative + A5P + PEP<br />
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}}
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== References ==
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<references/>
[[Category:Topic Page]]
[[Category:Topic Page]]

Current revision

Metallo Kdo-8-phosphate synthase tetramer complex with phosphoenolpyruvate, glycerol, Cl- (green), Na+ (large purple) and Mn+2 (small purple) ion, 3fyp

Drag the structure with the mouse to rotate

3D structures of Kdo-8-phosphate synthase

Updated on 11-October-2021

References

  1. ↑ Krosky DJ, Alm R, Berg M, Carmel G, Tummino PJ, Xu B, Yang W. Helicobacter pylori 3-deoxy-D-manno-octulosonate-8-phosphate (KDO-8-P) synthase is a zinc-metalloenzyme. Biochim Biophys Acta. 2002 Feb 11;1594(2):297-306. PMID:11904225
  2. ↑ Cochrane FC, Cookson TV, Jameson GB, Parker EJ. Reversing evolution: re-establishing obligate metal ion dependence in a metal-independent KDO8P synthase. J Mol Biol. 2009 Jul 24;390(4):646-61. Epub 2009 May 15. PMID:19447118 doi:10.1016/j.jmb.2009.05.014

Proteopedia Page Contributors and Editors (what is this?)

Michal Harel, Alexander Berchansky, Joel L. Sussman

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