PDBsum entry 1qb4

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Lyase PDB id
Protein chain
874 a.a. *
Waters ×81
* Residue conservation analysis
PDB id:
Name: Lyase
Title: Crystal structure of mn(2+)-bound phosphoenolpyruvate carboxylase
Structure: Phosphoenolpyruvate carboxylase. Chain: a. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: k12. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.60Å     R-factor:   0.221     R-free:   0.261
Authors: H.Matsumura,M.Terada,S.Shirakata,T.Inoue,T.Yoshinaga,K.Izui, Y.Kai
Key ref: H.Matsumura et al. (1999). Plausible phosphoenolpyruvate binding site revealed by 2.6 A structure of Mn2+-bound phosphoenolpyruvate carboxylase from Escherichia coli. FEBS Lett, 458, 93-96. PubMed id: 10481043
30-Apr-99     Release date:   01-May-02    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P00864  (CAPP_ECOLI) -  Phosphoenolpyruvate carboxylase
883 a.a.
874 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  


FEBS Lett 458:93-96 (1999)
PubMed id: 10481043  
Plausible phosphoenolpyruvate binding site revealed by 2.6 A structure of Mn2+-bound phosphoenolpyruvate carboxylase from Escherichia coli.
H.Matsumura, M.Terada, S.Shirakata, T.Inoue, T.Yoshinaga, K.Izui, Y.Kai.
We have determined the crystal structure of Mn2+-bound Escherichia coli phosphoenolpyruvate carboxylase (PEPC) using X-ray diffraction at 2.6 A resolution, and specified the location of enzyme-bound Mn2+, which is essential for catalytic activity. The electron density map reveals that Mn2+ is bound to the side chain oxygens of Glu-506 and Asp-543, and located at the top of the alpha/beta barrel in PEPC. The coordination sphere of Mn2+ observed in E. coli PEPC is similar to that of Mn2+ found in the pyruvate kinase structure. The model study of Mn2+-bound PEPC complexed with phosphoenolpyruvate (PEP) reveals that the side chains of Arg-396, Arg-581 and Arg-713 could interact with PEP.

Literature references that cite this PDB file's key reference

  PubMed id Reference
16624802 W.Xu, S.Ahmed, H.Moriyama, and R.Chollet (2006).
The importance of the strictly conserved, C-terminal glycine residue in phosphoenolpyruvate carboxylase for overall catalysis: mutagenesis and truncation of GLY-961 in the sorghum C4 leaf isoform.
  J Biol Chem, 281, 17238-17245.  
16102602 U.Sauer, and B.J.Eikmanns (2005).
The PEP-pyruvate-oxaloacetate node as the switch point for carbon flux distribution in bacteria.
  FEMS Microbiol Rev, 29, 765-794.  
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.  
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.  
12829271 D.G.Kehres, and M.E.Maguire (2003).
Emerging themes in manganese transport, biochemistry and pathogenesis in bacteria.
  FEMS Microbiol Rev, 27, 263-290.  
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.  
12084062 J.Mima, G.Jung, T.Onizuka, H.Ueno, and R.Hayashi (2002).
Amphipathic property of free thiol group contributes to an increase in the catalytic efficiency of carboxypeptidase Y.
  Eur J Biochem, 269, 3220-3225.  
12084063 L.F.García-Alles, and B.Erni (2002).
Synthesis of phosphoenol pyruvate (PEP) analogues and evaluation as inhibitors of PEP-utilizing enzymes.
  Eur J Biochem, 269, 3226-3236.  
11741915 L.F.Garcia-Alles, K.Flükiger, J.Hewel, R.Gutknecht, C.Siebold, S.Schürch, and B.Erni (2002).
Mechanism-based inhibition of enzyme I of the Escherichia coli phosphotransferase system. Cysteine 502 is an essential residue.
  J Biol Chem, 277, 6934-6942.  
12089331 S.Akhter, A.Vignini, Z.Wen, A.English, P.G.Wang, and B.Mutus (2002).
Evidence for S-nitrosothiol-dependent changes in fibrinogen that do not involve transnitrosation or thiolation.
  Proc Natl Acad Sci U S A, 99, 9172-9177.  
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.