PDBsum entry 1fiy

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Complex (lyase/inhibitor) PDB id
Protein chain
873 a.a. *
Waters ×39
* Residue conservation analysis
PDB id:
Name: Complex (lyase/inhibitor)
Title: Three-dimensional structure of phosphoenolpyruvate carboxyla escherichia coli at 2.8 a resolution
Structure: Phosphoenolpyruvate carboxylase. Chain: a. Synonym: pepc. Ec:
Source: Escherichia coli. Organism_taxid: 83333. Strain: k12
2.80Å     R-factor:   0.219     R-free:   0.259
Authors: Y.Kai,H.Matsumura,T.Inoue,K.Terada,Y.Nagara,T.Yoshinaga,A.Ki K.Izui
Key ref:
Y.Kai et al. (1999). Three-dimensional structure of phosphoenolpyruvate carboxylase: a proposed mechanism for allosteric inhibition. Proc Natl Acad Sci U S A, 96, 823-828. PubMed id: 9927652 DOI: 10.1073/pnas.96.3.823
02-May-98     Release date:   09-Feb-99    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P00864  (CAPP_ECOLI) -  Phosphoenolpyruvate carboxylase
883 a.a.
873 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Phosphoenolpyruvate carboxylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Phosphate + oxaloacetate = H2O + phosphoenolpyruvate + HCO3-
Bound ligand (Het Group name = ASP)
matches with 80.00% similarity
= H(2)O
+ phosphoenolpyruvate
+ HCO(3)(-)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytosol   1 term 
  Biological process     metabolic process   4 terms 
  Biochemical function     catalytic activity     4 terms  


DOI no: 10.1073/pnas.96.3.823 Proc Natl Acad Sci U S A 96:823-828 (1999)
PubMed id: 9927652  
Three-dimensional structure of phosphoenolpyruvate carboxylase: a proposed mechanism for allosteric inhibition.
Y.Kai, H.Matsumura, T.Inoue, K.Terada, Y.Nagara, T.Yoshinaga, A.Kihara, K.Tsumura, K.Izui.
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.
  Selected figure(s)  
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.
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21040799 A.Singh, K.Cher Soh, V.Hatzimanikatis, and R.T.Gill (2011).
Manipulating redox and ATP balancing for improved production of succinate in E. coli.
  Metab Eng, 13, 76-81.  
  21491491 L.Dharmarajan, J.L.Kraszewski, B.Mukhopadhyay, and P.W.Dunten (2011).
Structure of an archaeal-type phosphoenolpyruvate carboxylase sensitive to inhibition by aspartate.
  Proteins, 79, 1820-1829.
PDB code: 3odm
20645337 Villiers, L.Koekemoer, and E.Strauss (2010).
3-Fluoroaspartate and pyruvoyl-dependant aspartate decarboxylase: exploiting the unique characteristics of fluorine to probe reactivity and binding.
  Chemistry, 16, 10030-10041.  
19244229 A.Schmid, W.Neumayer, K.Trülzsch, L.Israel, A.Imhof, M.Roessle, G.Sauer, S.Richter, S.Lauw, E.Eylert, W.Eisenreich, J.Heesemann, and G.Wilharm (2009).
Cross-talk between type three secretion system and metabolism in Yersinia.
  J Biol Chem, 284, 12165-12177.  
  19923749 L.Dharmarajan, J.L.Kraszewski, B.Mukhopadhyay, and P.W.Dunten (2009).
Expression, purification and crystallization of an archaeal-type phosphoenolpyruvate carboxylase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 1193-1196.  
18266899 B.Jacobs, S.Engelmann, P.Westhoff, and U.Gowik (2008).
Evolution of C(4) phosphoenolpyruvate carboxylase in Flaveria: determinants for high tolerance towards the inhibitor L-malate.
  Plant Cell Environ, 31, 793-803.  
18059531 M.Zhao, X.Jia, C.Wang, Q.Li, K.Zhou, L.Wang, H.Liu, and S.Peng (2007).
PAK: an essential motif for forming beta-turn structures and exhibiting the thrombolytic effect of P6A and its analogs.
  Biochem Cell Biol, 85, 730-740.  
17614282 P.A.Christin, N.Salamin, V.Savolainen, M.R.Duvall, and G.Besnard (2007).
C4 Photosynthesis evolved in grasses via parallel adaptive genetic changes.
  Curr Biol, 17, 1241-1247.  
17894783 S.Gennidakis, S.Rao, K.Greenham, R.G.Uhrig, B.O'Leary, W.A.Snedden, C.Lu, and W.C.Plaxton (2007).
Bacterial- and plant-type phosphoenolpyruvate carboxylase polypeptides interact in the hetero-oligomeric Class-2 PEPC complex of developing castor oil seeds.
  Plant J, 52, 839-849.  
16283377 R.Sánchez, A.Flores, and F.J.Cejudo (2006).
Arabidopsis phosphoenolpyruvate carboxylase genes encode immunologically unrelated polypeptides and are differentially expressed in response to drought and salt stress.
  Planta, 223, 901-909.  
15262949 H.M.Patel, J.L.Kraszewski, and B.Mukhopadhyay (2004).
The phosphoenolpyruvate carboxylase from Methanothermobacter thermautotrophicus has a novel structure.
  J Bacteriol, 186, 5129-5137.  
15725057 K.Izui, H.Matsumura, T.Furumoto, and Y.Kai (2004).
Phosphoenolpyruvate carboxylase: a new era of structural biology.
  Annu Rev Plant Biol, 55, 69-84.  
15329673 P.R.Hall, R.Zheng, L.Antony, M.Pusztai-Carey, P.R.Carey, and V.C.Yee (2004).
Transcarboxylase 5S structures: assembly and catalytic mechanism of a multienzyme complex subunit.
  EMBO J, 23, 3621-3631.
PDB codes: 1rqb 1rqe 1rqh 1rr2 1s3h 1u5j
15516590 T.J.Ettema, K.S.Makarova, G.L.Jellema, H.J.Gierman, E.V.Koonin, M.A.Huynen, Vos, and J.van der Oost (2004).
Identification and functional verification of archaeal-type phosphoenolpyruvate carboxylase, a missing link in archaeal central carbohydrate metabolism.
  J Bacteriol, 186, 7754-7762.  
12966569 C.Yang, Q.Hua, T.Baba, H.Mori, and K.Shimizu (2003).
Analysis of Escherichia coli anaplerotic metabolism and its regulation mechanisms from the metabolic responses to altered dilution rates and phosphoenolpyruvate carboxykinase knockout.
  Biotechnol Bioeng, 84, 129-144.  
12837791 F.Schmitzberger, A.G.Smith, C.Abell, and T.L.Blundell (2003).
Comparative analysis of the Escherichia coli ketopantoate hydroxymethyltransferase crystal structure confirms that it is a member of the (betaalpha)8 phosphoenolpyruvate/pyruvate superfamily.
  J Bacteriol, 185, 4163-4171.  
10531501 H.Matsumura, T.Nagata, M.Terada, S.Shirakata, T.Inoue, T.Yoshinaga, Y.Ueno, H.Saze, K.Izui, and Y.Kai (1999).
Crystallization and preliminary x-ray diffraction studies of C4-form phosphoenolpyruvate carboxylase from maize.
  Acta Crystallogr D Biol Crystallogr, 55, 1937-1938.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.