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Kinase (transphosphorylating) PDB id
1ayl
Jmol
Contents
Protein chain
532 a.a. *
Ligands
OXL
ATP
Metals
_MG
Waters ×1035
* Residue conservation analysis
PDB id:
1ayl
Name: Kinase (transphosphorylating)
Title: Phosphoenolpyruvate carboxykinase
Structure: Phosphoenolpyruvate carboxykinase. Chain: a. Synonym: atp-oxaloacetate carboxy-lyase (atp). Other_details: ordered magnesium ion observed bound to atp
Source: Escherichia coli. Organism_taxid: 83333. Strain: k12
Biol. unit: Dimer (from PQS)
Resolution:
1.80Å     R-factor:   0.195     R-free:   0.234
Authors: L.W.Tari,U.Pugazenthi,H.Goldie,L.T.J.Delbaere
Key ref: L.W.Tari et al. (1996). Snapshot of an enzyme reaction intermediate in the structure of the ATP-Mg2+-oxalate ternary complex of Escherichia coli PEP carboxykinase. Nat Struct Biol, 3, 355-363. PubMed id: 8599762 DOI: 10.1038/nsb0496-355
Date:
07-Dec-95     Release date:   11-Jan-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P22259  (PCKA_ECOLI) -  Phosphoenolpyruvate carboxykinase [ATP]
Seq:
Struc: 		 
Seq:
Struc: 		540 a.a.
532 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.4.1.1.49  - Phosphoenolpyruvate carboxykinase (ATP).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + oxaloacetate = ADP + phosphoenolpyruvate + CO2
ATP
Bound ligand (Het Group name = ATP)
corresponds exactly 		+
oxaloacetate
Bound ligand (Het Group name = OXL)
matches with 50.00% similarity 		= ADP
 + phosphoenolpyruvate
 + CO(2)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     metabolic process   2 terms 
  Biochemical function     catalytic activity     8 terms  

 

 
    reference    
 
 
DOI no: 10.1038/nsb0496-355 Nat Struct Biol 3:355-363 (1996)
PubMed id: 8599762  
 
 
Snapshot of an enzyme reaction intermediate in the structure of the ATP-Mg2+-oxalate ternary complex of Escherichia coli PEP carboxykinase.
L.W.Tari, A.Matte, U.Pugazhenthi, H.Goldie, L.T.Delbaere.
 
  ABSTRACT  
 
We report the 1.8 A crystal structure of adenosine triphosphate (ATP)-magnesium-oxalate bound phosphoenolpyruvate carboxykinase (PCK) from Escherichia coli. ATP binding induces a 20 degree hinge-like rotation of the N- and C-terminal domains which closes the active-site cleft. PCK possesses a novel nucleotide-binding fold, particularly in the adenine-binding region, where the formation of a cis backbone torsion angle in a loop glycine residue promotes intimate contacts between the adenine-binding loop and adenine, while stabilizing a syn conformation of the base. This complex represents a reaction intermediate analogue along the pathway of the conversion of oxaloacetate to phosphoenolpyruvate, and provides insight into the mechanistic details of the chemical reaction catalysed by this enzyme.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20524049 E.Pérez, and E.Cardemil (2010).
Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase: the relevance of Glu299 and Leu460 for nucleotide binding.
  Protein J, 29, 299-305.  
19217394 A.R.Kinjo, and H.Nakamura (2009).
Comprehensive structural classification of ligand-binding motifs in proteins.
  Structure, 17, 234-246.  
19638345 G.M.Carlson, and T.Holyoak (2009).
Structural insights into the mechanism of phosphoenolpyruvate carboxykinase catalysis.
  J Biol Chem, 284, 27037-27041.  
18346928 I.Tobar, F.D.González-Nilo, A.M.Jabalquinto, and E.Cardemil (2008).
Relevance of Arg457 for the nucleotide affinity of Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase.
  Int J Biochem Cell Biol, 40, 1883-1889.  
18385384 L.Xie, and P.E.Bourne (2008).
Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments.
  Proc Natl Acad Sci U S A, 105, 5441-5446.  
17475535 J.J.Cotelesage, J.Puttick, H.Goldie, B.Rajabi, B.Novakovski, and L.T.Delbaere (2007).
How does an enzyme recognize CO2?
  Int J Biochem Cell Biol, 39, 1204-1210.
PDB codes: 2olq 2olr
17878158 V.Chaptal, F.Vincent, V.Gueguen-Chaignon, V.Monedero, S.Poncet, J.Deutscher, S.Nessler, and S.Morera (2007).
Structural analysis of the bacterial HPr kinase/phosphorylase V267F mutant gives insights into the allosteric regulation mechanism of this bifunctional enzyme.
  J Biol Chem, 282, 34952-34957.
PDB code: 2qmh
16788205 K.I.Varughese, I.Tsigelny, and H.Zhao (2006).
The crystal structure of beryllofluoride Spo0F in complex with the phosphotransferase Spo0B represents a phosphotransfer pretransition state.
  J Bacteriol, 188, 4970-4977.
PDB code: 2ftk
15890557 J.J.Cotelesage, L.Prasad, J.G.Zeikus, M.Laivenieks, and L.T.Delbaere (2005).
Crystal structure of Anaerobiospirillum succiniciproducens PEP carboxykinase reveals an important active site loop.
  Int J Biochem Cell Biol, 37, 1829-1837.
PDB codes: 1ytm 1yvy
16239727 M.Sugahara, N.Ohshima, Y.Ukita, M.Sugahara, and N.Kunishima (2005).
Structure of ATP-dependent phosphoenolpyruvate carboxykinase from Thermus thermophilus HB8 showing the structural basis of induced fit and thermostability.
  Acta Crystallogr D Biol Crystallogr, 61, 1500-1507.
PDB codes: 1j3b 1xkv
15983413 Y.A.Leduc, L.Prasad, M.Laivenieks, J.G.Zeikus, and L.T.Delbaere (2005).
Structure of PEP carboxykinase from the succinate-producing Actinobacillus succinogenes: a new conserved active-site motif.
  Acta Crystallogr D Biol Crystallogr, 61, 903-912.
PDB codes: 1ygg 1ylh
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
12876308 K.Kinoshita, and H.Nakamura (2003).
Identification of protein biochemical functions by similarity search using the molecular surface database eF-site.
  Protein Sci, 12, 1589-1595.  
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.  
11796714 A.Galinier, J.P.Lavergne, C.Geourjon, S.Fieulaine, S.Nessler, and J.M.Jault (2002).
A new family of phosphotransferases with a P-loop motif.
  J Biol Chem, 277, 11362-11367.  
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.  
  11943595 M.V.Encinas, F.D.González-Nilo, J.M.Andreu, C.Alfonso, and E.Cardemil (2002).
Urea-induced unfolding studies of free- and ligand-bound tetrameric ATP-dependent Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase. Influence of quaternary structure on protein conformational stability.
  Int J Biochem Cell Biol, 34, 645-656.  
  11188689 T.Zhou, M.Daugherty, N.V.Grishin, A.L.Osterman, and H.Zhang (2000).
Structure and mechanism of homoserine kinase: prototype for the GHMP kinase superfamily.
  Structure, 8, 1247-1257.
PDB codes: 1fwk 1fwl
11042161 Y.Wang, S.Bryant, R.Tatusov, and T.Tatusova (2000).
Links from genome proteins to known 3-D structures.
  Genome Res, 10, 1643-1647.  
  10217755 M.Inui, K.Nakata, J.H.Roh, K.Zahn, and H.Yukawa (1999).
Molecular and functional characterization of the Rhodopseudomonas palustris no. 7 phosphoenolpyruvate carboxykinase gene.
  J Bacteriol, 181, 2689-2696.  
  9562560 A.Matte, L.W.Tari, and L.T.Delbaere (1998).
How do kinases transfer phosphoryl groups?
  Structure, 6, 413-419.  
9792679 E.H.Bursey, and B.K.Burgess (1998).
The role of methionine 156 in cross-subunit nucleotide interactions in the iron protein of nitrogenase.
  J Biol Chem, 273, 29678-29685.  
9572844 H.Krautwurst, S.Bazaes, F.D.González, A.M.Jabalquinto, P.A.Frey, and E.Cardemil (1998).
The strongly conserved lysine 256 of Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase is essential for phosphoryl transfer.
  Biochemistry, 37, 6295-6302.  
9843365 I.I.Mathews, M.D.Erion, and S.E.Ealick (1998).
Structure of human adenosine kinase at 1.5 A resolution.
  Biochemistry, 37, 15607-15620.
PDB code: 1bx4
9920388 L.Carrasco, F.D.González, and E.Cardemil (1998).
Interaction of adenosine nucleotide analogs with Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase.
  Biochim Biophys Acta, 1429, 93.  
9572839 T.M.Larsen, M.M.Benning, I.Rayment, and G.H.Reed (1998).
Structure of the bis(Mg2+)-ATP-oxalate complex of the rabbit muscle pyruvate kinase at 2.1 A resolution: ATP binding over a barrel.
  Biochemistry, 37, 6247-6255.
PDB codes: 1a49 1a5u
  9172347 M.Laivenieks, C.Vieille, and J.G.Zeikus (1997).
Cloning, sequencing, and overexpression of the Anaerobiospirillum succiniciproducens phosphoenolpyruvate carboxykinase (pckA) gene.
  Appl Environ Microbiol, 63, 2273-2280.  
  8994968 R.L.Kingston, R.K.Scopes, and E.N.Baker (1996).
The structure of glucose-fructose oxidoreductase from Zymomonas mobilis: an osmoprotective periplasmic enzyme containing non-dissociable NADP.
  Structure, 4, 1413-1428.
PDB code: 1ofg
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 codes are shown on the right.