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PDBsum entry 1k3d
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protein ligands metals links
Lyase PDB id
1k3d

 

 

 

 

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Contents
Protein chain
535 a.a. *
Ligands
ADP-AF3
Metals
_MG
Waters ×275
* Residue conservation analysis
PDB id:
1k3d
Name: Lyase
Title: Phosphoenolpyruvate carboxykinase in complex with adp and alf3
Structure: Phosphoenolpyruvate carboxykinase. Chain: a. Synonym: pep carboxykinase, phosphoenolpyruvate carboxylase, pepck. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: pcka. Expressed in: escherichia coli k12. Expression_system_taxid: 83333.
Resolution:
2.00Å     R-factor:   0.196     R-free:   0.266
Authors: A.M.Sudom,L.Prasad,H.Goldie,L.T.J.Delbaere
Key ref:
A.M.Sudom et al. (2001). The phosphoryl-transfer mechanism of Escherichia coli phosphoenolpyruvate carboxykinase from the use of AlF(3). J Mol Biol, 314, 83-92. PubMed id: 11724534 DOI: 10.1006/jmbi.2001.5120
Date:
02-Oct-01     Release date:   19-Dec-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P22259  (PCKA_ECOLI) -  Phosphoenolpyruvate carboxykinase (ATP) from Escherichia coli (strain K12)
Seq:
Struc: 		 
Seq:
Struc: 		540 a.a.
535 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.4.1.1.49  - phosphoenolpyruvate carboxykinase (ATP).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: oxaloacetate + ATP = phosphoenolpyruvate + ADP + CO2
oxaloacetate
 + ATP
 =
phosphoenolpyruvate
Bound ligand (Het Group name = ADP)
corresponds exactly 		+ ADP
 + CO2
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.2001.5120 J Mol Biol 314:83-92 (2001)
PubMed id: 11724534  
 
 
The phosphoryl-transfer mechanism of Escherichia coli phosphoenolpyruvate carboxykinase from the use of AlF(3).
A.M.Sudom, L.Prasad, H.Goldie, L.T.Delbaere.
 
  ABSTRACT  
 
The mechanism of reversible transfer of the gamma-phosphate group of ATP by Escherichia coli phosphoenolpyruvate carboxykinase (PCK) on to its substrate is of great interest. It is known that metallofluorides are accurate analogs of the transition state in the context of kinase mechanisms. Therefore, two complexes of PCK, one with AlF(3), Mg(2+) and ADP (complex I), the other with AlF(3), Mg(2+), ADP and pyruvate (complex II) were crystallized. The X-ray crystal structures of these two complexes were determined at 2.0 A resolution. The Al atom has trigonal bipyramidal geometry that mimics the transition state of phosphoryl transfer. The Al atom is at a distance of 2.8 A and 2.9 A from an oxygen atom of the beta-phosphoryl group of ADP in complex I and II, respectively. A water molecule in complex I and an oxygen atom of the pyruvate in complex II are located along the axis of the trigonal bipyramid on the side opposite to the beta-phosphoryl oxygen with respect to the equatorial plane, suggesting that the complexes are close mimics of the transition state. Along with the presence of positively charged species around the AlF(3) moiety, these results indicate that phosphoryl transfer occurs via a direct displacement mechanism with associative qualities.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. The associative (SN2-like) versus dissociative (SN1-like) mechanisms of phosphoryl transfer. As can be seen in the associative state, one bond is formed between the incoming nucleophile and attacked phosphorus atom concurrently with the existing bond between Pg and the b, g-bridging oxygen. The dissociative state first involves bond breaking between Pg and the b, g-bridging oxygen, then bond formation occurs. The two states also differ in geometry and charge distribution, as the associative case involves a pentagonal bipyramidal structure ( -3) and the dissociative case involves a planar, trigonal phosphorane ( -1). 		Figure 4.
Figure 4. Detailed diagram illustrating AlF[3] binding in the active site region of the ADP-Mg2+-AlF[3] E. coli PCK quaternary complex. Note that the fluorine atoms interact primarily with basic residues or Mg2+. The aluminum atom is close to an oxygen atom of the b-phosphoryl group of ATP. Mg2+ is the light blue sphere, the aluminum atom is colored pink, the fluorine atoms are colored green. (a) PCK-ADP-AlF[3]-Mg2+ complex (complex I). (b) PCK-ADP-AlF[3]-Mg2+-pyruvate complex (complex II).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 314, 83-92) copyright 2001.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20513959 N.Asanuma, K.Kanada, Y.Arai, K.Yoshizawa, T.Ichikawa, and T.Hino (2010).
Molecular characterization and significance of phosphoenolpyruvate carboxykinase in a ruminal bacterium, Streptococcus bovis.
  J Gen Appl Microbiol, 56, 121-127.  
19638345 G.M.Carlson, and T.Holyoak (2009).
Structural insights into the mechanism of phosphoenolpyruvate carboxykinase catalysis.
  J Biol Chem, 284, 27037-27041.  
19194751 N.Asanuma, K.Yoshizawa, K.Kanada, and T.Hino (2009).
Molecular and biochemical characterization of phosphoenolpyruvate carboxykinase in the ruminal bacterium Ruminococcus albus.
  Curr Microbiol, 58, 416-420.  
19021757 L.Dharmarajan, C.L.Case, P.Dunten, and B.Mukhopadhyay (2008).
Tyr235 of human cytosolic phosphoenolpyruvate carboxykinase influences catalysis through an anion-quadrupole interaction with phosphoenolpyruvate carboxylate.
  FEBS J, 275, 5810-5819.  
  19461981 S.Aich, and L.T.Delbaere (2007).
Phylogenetic Study of the Evolution of PEP-Carboxykinase.
  Evol Bioinform Online, 3, 333-340.  
12837799 A.Sudom, R.Walters, L.Pastushok, D.Goldie, L.Prasad, L.T.Delbaere, and H.Goldie (2003).
Mechanisms of activation of phosphoenolpyruvate carboxykinase from Escherichia coli by Ca2+ and of desensitization by trypsin.
  J Bacteriol, 185, 4233-4242.
PDB code: 1os1
12837773 S.Nessler, S.Fieulaine, S.Poncet, A.Galinier, J.Deutscher, and J.Janin (2003).
HPr kinase/phosphorylase, the sensor enzyme of catabolite repression in Gram-positive bacteria: structural aspects of the enzyme and the complex with its protein substrate.
  J Bacteriol, 185, 4003-4010.  
12383254 M.V.Encinas, F.D.González-Nilo, H.Goldie, and E.Cardemil (2002).
Ligand interactions and protein conformational changes of phosphopyridoxyl-labeled Escherichia coli phosphoenolpyruvate carboxykinase determined by fluorescence spectroscopy.
  Eur J Biochem, 269, 4960-4968.  
11896404 Madhusudan, P.Akamine, N.H.Xuong, and S.S.Taylor (2002).
Crystal structure of a transition state mimic of the catalytic subunit of cAMP-dependent protein kinase.
  Nat Struct Biol, 9, 273-277.
PDB code: 1l3r
12359875 S.Fieulaine, S.Morera, S.Poncet, I.Mijakovic, A.Galinier, J.Janin, J.Deutscher, and S.Nessler (2002).
X-ray structure of a bifunctional protein kinase in complex with its protein substrate HPr.
  Proc Natl Acad Sci U S A, 99, 13437-13441.
PDB codes: 1kkl 1kkm
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.

 

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