1g7u: Difference between revisions

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New page: left|200px<br /><applet load="1g7u" size="450" color="white" frame="true" align="right" spinBox="true" caption="1g7u, resolution 2.8Å" /> '''CRYSTAL STRUCTURES OF...
 
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[[Image:1g7u.jpg|left|200px]]<br /><applet load="1g7u" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1g7u, resolution 2.8&Aring;" />
'''CRYSTAL STRUCTURES OF KDO8P SYNTHASE IN ITS BINARY COMPLEX WITH SUBSTRATE PHOSPHOENOL PYRUVATE'''<br />


==Overview==
==CRYSTAL STRUCTURES OF KDO8P SYNTHASE IN ITS BINARY COMPLEX WITH SUBSTRATE PHOSPHOENOL PYRUVATE==
The crystal structures of 3-deoxy-D-manno-2-octulosonate-8-phosphate, synthase (KDOPS) from Escherichia coli complexed with the substrate, phosphoenolpyruvate (PEP) and with a mechanism-based inhibitor (K(d) = 0.4, microM) were determined by molecular replacement using X-ray diffraction, data to 2.8 and 2.3 A resolution, respectively. Both the KDOPS.PEP and, KDOPS.inhibitor complexes crystallize in the cubic space group I23 with, cell constants a = b = c = 117.9 and 117.6 A, respectively, and one, subunit per asymmetric unit. The two structures are nearly identical, and, superposition of their Calpha atoms indicates an rms difference of 0.41 A., The PEP in the KDOPS.PEP complex is anchored to the enzyme in a, conformation that blocks its si face and leaves its re face largely devoid, of contacts. This results from KDOPS's selective choice of a PEP conformer, in which the phosphate group of PEP is extended toward the si face., Furthermore, the structure reveals that the bridging (P-O-C) oxygen atom, and the carboxylate group of PEP are not strongly hydrogen-bonded to the, enzyme. The resulting high degree of negative charge on the carboxylate, group of PEP would then suggest that the condensation step between PEP and, D-arabinose-5-phosphate (A5P) should proceed in a stepwise fashion through, the intermediacy of a transient oxocarbenium ion at C2 of PEP. The, molecular structural results are discussed in light of the chemically, similar but mechanistically distinct reaction that is catalyzed by the, enzyme 3-deoxy-D-arabino-2-heptulosonate-7-phosphate synthase and in light, of the preferred enzyme-bound states of the substrate A5P.
<StructureSection load='1g7u' size='340' side='right'caption='[[1g7u]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1g7u]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G7U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1G7U 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]] 2.8&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</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=1g7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g7u OCA], [https://pdbe.org/1g7u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1g7u RCSB], [https://www.ebi.ac.uk/pdbsum/1g7u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1g7u ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/KDSA_ECOLI KDSA_ECOLI] Synthesis of KDO 8-P which is required for lipid A maturation and cellular growth.[HAMAP-Rule:MF_00056]
== 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/g7/1g7u_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=1g7u ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1G7U is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with PEP as [http://en.wikipedia.org/wiki/ligand ligand]. 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=1G7U OCA].
*[[Kdo-8-phosphate synthase|Kdo-8-phosphate synthase]]
 
__TOC__
==Reference==
</StructureSection>
Crystal structures of KDOP synthase in its binary complexes with the substrate phosphoenolpyruvate and with a mechanism-based inhibitor., Asojo O, Friedman J, Adir N, Belakhov V, Shoham Y, Baasov T, Biochemistry. 2001 May 29;40(21):6326-34. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11371194 11371194]
[[Category: 3-deoxy-8-phosphooctulonate synthase]]
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Adir, N.]]
[[Category: Adir N]]
[[Category: Asojo, O.A.]]
[[Category: Asojo OA]]
[[Category: Baasov, T.]]
[[Category: Baasov T]]
[[Category: Belakhov, V.]]
[[Category: Belakhov V]]
[[Category: Friedman, J.M.]]
[[Category: Friedman JM]]
[[Category: Shoham, Y.]]
[[Category: Shoham Y]]
[[Category: PEP]]
[[Category: beta-alpha-barrels]]
[[Category: lipopolysaccharide]]
[[Category: lyase]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 15:47:45 2007''

Latest revision as of 10:23, 7 February 2024

CRYSTAL STRUCTURES OF KDO8P SYNTHASE IN ITS BINARY COMPLEX WITH SUBSTRATE PHOSPHOENOL PYRUVATECRYSTAL STRUCTURES OF KDO8P SYNTHASE IN ITS BINARY COMPLEX WITH SUBSTRATE PHOSPHOENOL PYRUVATE

Structural highlights

1g7u is a 1 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.8Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

KDSA_ECOLI Synthesis of KDO 8-P which is required for lipid A maturation and cellular growth.[HAMAP-Rule:MF_00056]

Evolutionary Conservation

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

See Also

1g7u, resolution 2.80Å

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