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PDBsum entry 1fiy

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Complex (lyase/inhibitor) PDB id
1fiy
Jmol
Contents
Protein chain
873 a.a.
Ligands
ASP
Waters ×39

References listed in PDB file
Key reference
Title Three-Dimensional structure of phosphoenolpyruvate carboxylase: a proposed mechanism for allosteric inhibition.
Authors Y.Kai, H.Matsumura, T.Inoue, K.Terada, Y.Nagara, T.Yoshinaga, A.Kihara, K.Tsumura, K.Izui.
Ref. Proc Natl Acad Sci U S A, 1999, 96, 823-828. [DOI no: 10.1073/pnas.96.3.823]
PubMed id 9927652
Abstract
The crystal structure of phosphoenolpyruvate carboxylase (PEPC; EC 4. 1.1.31) has been determined by x-ray diffraction methods at 2.8-A resolution by using Escherichia coli PEPC complexed with L-aspartate, an allosteric inhibitor of all known PEPCs. The four subunits are arranged in a "dimer-of-dimers" form with respect to subunit contact, resulting in an overall square arrangement. The contents of alpha-helices and beta-strands are 65% and 5%, respectively. All of the eight beta-strands, which are widely dispersed in the primary structure, participate in the formation of a single beta-barrel. Replacement of a conserved Arg residue (Arg-438) in this linkage with Cys increased the tendency of the enzyme to dissociate into dimers. The location of the catalytic site is likely to be near the C-terminal side of the beta-barrel. The binding site for L-aspartate is located about 20 A away from the catalytic site, and four residues (Lys-773, Arg-832, Arg-587, and Asn-881) are involved in effector binding. The participation of Arg-587 is unexpected, because it is known to be catalytically essential. Because this residue is in a highly conserved glycine-rich loop, which is characteristic of PEPC, L-aspartate seemingly causes inhibition by removing this glycine-rich loop from the catalytic site. There is another mobile loop from Lys-702 to Gly-708 that is missing in the crystal structure. The importance of this loop in catalytic activity was also shown. Thus, the crystal-structure determination of PEPC revealed two mobile loops bearing the enzymatic functions and accompanying allosteric inhibition by L-aspartate.
Figure 6.
Fig. 6. Stereoview of the probable active site of PEPC. H138, R396, K546, H579, R581, R587, R699, and aspartate are shown in ball-and-stick representation. The figure is drawn in the same orientation as Fig. 3a. The loop region of GRGGSIGRGG is shown in blue. The missing loop from Lys-702 to Gly-708 is shown as dots.
Figure 7.
Fig. 7. (a) The C-terminal helix ( 40), shown in blue, is embedded in the PEPC monomer. The figure was produced with MOLSCRIPT (37) and RASTER3D (38). (b) The molecular surface, omitting the C-terminal helix coordinates, was calculated with GRASP (25). The figure is shown in the same orientation as a.
Secondary reference #1
Title First crystallization of a phosphoenolpyruvate carboxylase from escherichia coli.
Authors M.Inoue, M.Hayashi, M.Sugimoto, S.Harada, Y.Kai, N.Kasai, K.Terada, K.Izui.
Ref. J Mol Biol, 1989, 208, 509-510.
PubMed id 2677392
Abstract
PROCHECK
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