1g7u: Difference between revisions
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|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</scene> | |LIGAND= <scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</scene> | ||
|ACTIVITY= [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] | |ACTIVITY= <span class='plainlinks'>[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] </span> | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY=[[1g7v|1G7V]] | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1g7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g7u OCA], [http://www.ebi.ac.uk/pdbsum/1g7u PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1g7u RCSB]</span> | |||
}} | }} | ||
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[[Category: Friedman, J M.]] | [[Category: Friedman, J M.]] | ||
[[Category: Shoham, Y.]] | [[Category: Shoham, Y.]] | ||
[[Category: beta-alpha-barrel]] | [[Category: beta-alpha-barrel]] | ||
[[Category: lipopolysaccharide]] | [[Category: lipopolysaccharide]] | ||
[[Category: lyase]] | [[Category: lyase]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 20:38:25 2008'' | ||
Revision as of 20:38, 30 March 2008
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| , resolution 2.8Å | |||||||
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| Ligands: | |||||||
| Activity: | 3-deoxy-8-phosphooctulonate synthase, with EC number 2.5.1.55 | ||||||
| Related: | 1G7V
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
CRYSTAL STRUCTURES OF KDO8P SYNTHASE IN ITS BINARY COMPLEX WITH SUBSTRATE PHOSPHOENOL PYRUVATE
OverviewOverview
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.
About this StructureAbout this Structure
1G7U is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.
ReferenceReference
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:11371194
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