1jcy: Difference between revisions

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New page: left|200px<br /><applet load="1jcy" size="450" color="white" frame="true" align="right" spinBox="true" caption="1jcy, resolution 1.90Å" /> '''Aquifex aeolicus KDO...
 
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[[Image:1jcy.gif|left|200px]]<br /><applet load="1jcy" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1jcy, resolution 1.90&Aring;" />
'''Aquifex aeolicus KDO8P synthase in complex with R5P, PEP and Cadmium'''<br />


==Overview==
==Aquifex aeolicus KDO8P synthase in complex with R5P, PEP and Cadmium==
We have determined the crystal structures of the metalloenzyme, 3-deoxy-D-manno-octulosonate 8-phosphate (KDO8P) synthase from Aquifex, aeolicus in complex with phosphoenolpyruvate (PEP) and ribose 5-phosphate, (R5P), and with a bisubstrate inhibitor that mimics the postulated linear, reaction intermediate. R5P, which is not a substrate for KDO8P synthase, binds in a manner similar to that of arabinose 5-phosphate (A5P), which is, the natural substrate. The lack of reactivity of R5P appears to be, primarily a consequence of the loss of a water molecule coordinated to, Cd(2+) and located on the si side of PEP. This water molecule is no longer, present because it cannot form a hydrogen bond with C2-OH(R5P), which is, oriented in a different direction from C2-OH(A5P). The bisubstrate, inhibitor binds with its phosphate and phosphonate moieties occupying the, positions of the phosphate groups of A5P and PEP, respectively. One of the, inhibitor hydroxyls replaces water as a ligand of Cd(2+). The current work, supports a mechanism for the synthesis of KDO8P, in which a hydroxide ion, on the si side of PEP attacks C2(PEP), forming a tetrahedral-like, intermediate with a buildup of negative charge at C3(PEP). The ensuing, condensation of C3(PEP) with C1(A5P) would be favored by a proton transfer, from the phosphate moiety of PEP to the aldehyde carbonyl of A5P to, generate the hydroxyl. Overall, the process can be described as a syn, addition of water and A5P to the si side of PEP.
<StructureSection load='1jcy' size='340' side='right'caption='[[1jcy]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1jcy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JCY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JCY FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=R5P:RIBOSE-5-PHOSPHATE'>R5P</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=1jcy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jcy OCA], [https://pdbe.org/1jcy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jcy RCSB], [https://www.ebi.ac.uk/pdbsum/1jcy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jcy ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/KDSA_AQUAE KDSA_AQUAE]
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jc/1jcy_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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=1jcy ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1JCY is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus] with R5P, CD, PO4 and PEP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/3-deoxy-8-phosphooctulonate_synthase 3-deoxy-8-phosphooctulonate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.55 2.5.1.55] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1JCY OCA].
*[[Kdo-8-phosphate synthase|Kdo-8-phosphate synthase]]
 
__TOC__
==Reference==
</StructureSection>
Structures of Aquifex aeolicus KDO8P synthase in complex with R5P and PEP, and with a bisubstrate inhibitor: role of active site water in catalysis., Wang J, Duewel HS, Woodard RW, Gatti DL, Biochemistry. 2001 Dec 25;40(51):15676-83. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11747443 11747443]
[[Category: 3-deoxy-8-phosphooctulonate synthase]]
[[Category: Aquifex aeolicus]]
[[Category: Aquifex aeolicus]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Duewel, H.S.]]
[[Category: Duewel HS]]
[[Category: Gatti, D.L.]]
[[Category: Gatti DL]]
[[Category: Wang, J.]]
[[Category: Wang J]]
[[Category: Woodard, R.W.]]
[[Category: Woodard RW]]
[[Category: CD]]
[[Category: PEP]]
[[Category: PO4]]
[[Category: R5P]]
[[Category: beta/alpha barrel]]
[[Category: kdo]]
[[Category: kdo8p]]
[[Category: kdo8ps]]
[[Category: pep]]
[[Category: r5p]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 18:07:07 2007''

Latest revision as of 10:38, 7 February 2024

Aquifex aeolicus KDO8P synthase in complex with R5P, PEP and CadmiumAquifex aeolicus KDO8P synthase in complex with R5P, PEP and Cadmium

Structural highlights

1jcy is a 2 chain structure with sequence from Aquifex aeolicus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.9Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

KDSA_AQUAE

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1jcy, resolution 1.90Å

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
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