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PDBsum entry 1pky

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protein Protein-protein interface(s) links
Phosphotransferase PDB id
1pky
Jmol PyMol
Contents
Protein chains
464 a.a. *
433 a.a. *
Waters ×520
* Residue conservation analysis
PDB id:
1pky
Name: Phosphotransferase
Title: Pyruvate kinase from e. Coli in the t-state
Structure: Pyruvate kinase. Chain: a, b, c, d. Other_details: t state
Source: Escherichia coli. Organism_taxid: 562
Biol. unit: Tetramer (from PQS)
Resolution:
2.50Å     R-factor:   0.203     R-free:   0.305
Authors: A.Mattevi
Key ref:
A.Mattevi et al. (1995). Crystal structure of Escherichia coli pyruvate kinase type I: molecular basis of the allosteric transition. Structure, 3, 729-741. PubMed id: 8591049 DOI: 10.1016/S0969-2126(01)00207-6
Date:
27-Apr-95     Release date:   07-Dec-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0AD61  (KPYK1_ECOLI) -  Pyruvate kinase I
Seq:
Struc:
470 a.a.
464 a.a.*
Protein chain
Pfam   ArchSchema ?
P0AD61  (KPYK1_ECOLI) -  Pyruvate kinase I
Seq:
Struc:
470 a.a.
433 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D: E.C.2.7.1.40  - Pyruvate kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + pyruvate = ADP + phosphoenolpyruvate
ATP
+ pyruvate
= ADP
+ phosphoenolpyruvate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   2 terms 
  Biological process     metabolic process   5 terms 
  Biochemical function     catalytic activity     10 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(01)00207-6 Structure 3:729-741 (1995)
PubMed id: 8591049  
 
 
Crystal structure of Escherichia coli pyruvate kinase type I: molecular basis of the allosteric transition.
A.Mattevi, G.Valentini, M.Rizzi, M.L.Speranza, M.Bolognesi, A.Coda.
 
  ABSTRACT  
 
BACKGROUND: Pyruvate kinase (PK) plays a major role in the regulation of glycolysis. Its catalytic activity is controlled by the substrate phosphoenolpyruvate and by one or more allosteric effectors. The crystal structures of the non-allosteric PKs from cat and rabbit muscle are known. We have determined the three-dimensional structure of the allosteric type I PK from Escherichia coli, in order to study the mechanism of allosteric regulation. RESULTS: The 2.5 A resolution crystal structure of the unligated type I PK in the inactive T-state shows that each subunit of the homotetrameric enzyme comprises a (beta/alpha)8-barrel domain, a flexible beta-barrel domain and a C-terminal domain. The allosteric and active sites are located at the domain interfaces. Comparison of the T-state E. coli PK with the non-allosteric muscle enzyme, which is thought to adopt a conformation similar to the active R-state, reveals differences in the orientations of the beta-barrel and C-terminal domains of each subunit, which are rotated by 17 degrees and 15 degrees, respectively. Moreover, the relative orientation of the four subunits differs by about 16 degrees in the two enzymes. Highly conserved residues at the subunit interfaces couple these movements to conformational changes in the substrate and allosteric effector binding sites. The subunit rotations observed in the T-state PK induce a shift in loop 6 of the (beta/alpha)8-barrel domain, leading to a distortion of the phosphoenolpyruvate-binding site accounting for the low substrate affinity of the T-state enzyme. CONCLUSIONS: Our results suggest that allosteric control of PK is accomplished through remarkable domain and subunit rotations. On transition from the T- to the R-state all 12 domains of the functional tetramer modify their relative orientations. These concerted motions are the molecular basis of the coupling between the active centre and the allosteric site.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. The final 2F[o] –F[c] electron-density map showing the conformation of residues 311–314 on loop 8 of subunit 2. Ser312 is the only residue which in all four subunits has an energetically unfavourable (φ, ψ) pair. The map is contoured at the 1σ level. Carbon atoms are shown in yellow, oxygens in red, nitrogens in blue. Figure 1. The final 2F[o] –F[c] electron-density map showing the conformation of residues 311–314 on loop 8 of subunit 2. Ser312 is the only residue which in all four subunits has an energetically unfavourable (φ, ψ) pair. The map is contoured at the 1σ level. Carbon atoms are shown in yellow, oxygens in red, nitrogens in blue. (Figure produced using O [[3]35].)
Figure 2.
Figure 2. Ribbon diagram of the structure of one PK subunit. Loop 6 of the (β/α)[8]-barrel is shown in green. Lys382 is close to the binding site for the allosteric effector fructose-1,6-bisphosphate (FBP) [12] and its Cα atom is indicated by a sphere. The Cα atoms of Phe345 and Leu352 are connected by a dashed line because residues 346–351 are disordered and not visible in the electron-density map. The view is approximately along the p axis of the tetramer. Figure 2. Ribbon diagram of the structure of one PK subunit. Loop 6 of the (β/α)[8]-barrel is shown in green. Lys382 is close to the binding site for the allosteric effector fructose-1,6-bisphosphate (FBP) [[3]12] and its Cα atom is indicated by a sphere. The Cα atoms of Phe345 and Leu352 are connected by a dashed line because residues 346–351 are disordered and not visible in the electron-density map. The view is approximately along the p axis of the tetramer. (Figure drawn using MOLSCRIPT [[4]45].)
 
  The above figures are reprinted by permission from Cell Press: Structure (1995, 3, 729-741) copyright 1995.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20856875 R.Bakszt, A.Wernimont, A.Allali-Hassani, M.W.Mok, T.Hills, R.Hui, and J.C.Pizarro (2010).
The crystal structure of Toxoplasma gondii pyruvate kinase 1.
  PLoS One, 5, e12736.
PDB codes: 3eoe 3gg8
20441757 S.Kumar, and A.Barth (2010).
Phosphoenolpyruvate and Mg2+ binding to pyruvate kinase monitored by infrared spectroscopy.
  Biophys J, 98, 1931-1940.  
19467627 A.W.Fenton, and M.Hutchinson (2009).
The pH dependence of the allosteric response of human liver pyruvate kinase to fructose-1,6-bisphosphate, ATP, and alanine.
  Arch Biochem Biophys, 484, 16-23.  
19265196 K.Akhtar, V.Gupta, A.Koul, N.Alam, R.Bhat, and R.N.Bamezai (2009).
Differential behavior of missense mutations in the intersubunit contact domain of the human pyruvate kinase m2 isozyme.
  J Biol Chem, 284, 11971-11981.  
19085939 R.van Wijk, E.G.Huizinga, A.C.van Wesel, B.A.van Oirschot, M.A.Hadders, and W.W.van Solinge (2009).
Fifteen novel mutations in PKLR associated with pyruvate kinase (PK) deficiency: structural implications of amino acid substitutions in PK.
  Hum Mutat, 30, 446-453.  
18326043 T.Saito, M.Nishi, M.I.Lim, B.Wu, T.Maeda, H.Hashimoto, T.Takeuchi, D.S.Roos, and T.Asai (2008).
A novel GDP-dependent pyruvate kinase isozyme from Toxoplasma gondii localizes to both the apicoplast and the mitochondrion.
  J Biol Chem, 283, 14041-14052.  
17360088 A.Zanella, E.Fermo, P.Bianchi, L.R.Chiarelli, and G.Valentini (2007).
Pyruvate kinase deficiency: the genotype-phenotype association.
  Blood Rev, 21, 217-231.  
17654506 M.F.Raphaël, R.Van Wijk, J.J.Schweizer, N.A.Schouten-van Meeteren, A.Kindermann, W.W.van Solinge, and F.J.Smiers (2007).
Pyruvate kinase deficiency associated with severe liver dysfunction in the newborn.
  Am J Hematol, 82, 1025-1028.  
18027374 S.S.Kharalkar, G.S.Joshi, F.N.Musayev, M.Fornabaio, D.J.Abraham, and M.K.Safo (2007).
Identification of novel allosteric regulators of human-erythrocyte pyruvate kinase.
  Chem Biodivers, 4, 2603-2617.  
16540430 D.C.Pendergrass, R.Williams, J.B.Blair, and A.W.Fenton (2006).
Mining for allosteric information: natural mutations and positional sequence conservation in pyruvate kinase.
  IUBMB Life, 58, 31-38.  
15982340 A.Zanella, E.Fermo, P.Bianchi, and G.Valentini (2005).
Red cell pyruvate kinase deficiency: molecular and clinical aspects.
  Br J Haematol, 130, 11-25.  
15953013 E.Fermo, P.Bianchi, L.R.Chiarelli, F.Cotton, C.Vercellati, K.Writzl, K.Baker, I.Hann, R.Rodwell, G.Valentini, and A.Zanella (2005).
Red cell pyruvate kinase deficiency: 17 new mutations of the PK-LR gene.
  Br J Haematol, 129, 839-846.  
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.  
12654928 U.Johnsen, T.Hansen, and P.Schonheit (2003).
Comparative analysis of pyruvate kinases from the hyperthermophilic archaea Archaeoglobus fulgidus, Aeropyrum pernix, and Pyrobaculum aerophilum and the hyperthermophilic bacterium Thermotoga maritima: unusual regulatory properties in hyperthermophilic archaea.
  J Biol Chem, 278, 25417-25427.  
11994161 E.R.Iliffe-Lee, and G.McClarty (2002).
Pyruvate kinase from Chlamydia trachomatis is activated by fructose-2,6-bisphosphate.
  Mol Microbiol, 44, 819-828.  
11960989 G.Valentini, L.R.Chiarelli, R.Fortin, M.Dolzan, A.Galizzi, D.J.Abraham, C.Wang, P.Bianchi, A.Zanella, and A.Mattevi (2002).
Structure and function of human erythrocyte pyruvate kinase. Molecular basis of nonspherocytic hemolytic anemia.
  J Biol Chem, 277, 23807-23814.
PDB codes: 2vgb 2vgf 2vgg 2vgi
11807949 H.Uchikoba, S.Fushinobu, T.Wakagi, M.Konno, H.Taguchi, and H.Matsuzawa (2002).
Crystal structure of non-allosteric L-lactate dehydrogenase from Lactobacillus pentosus at 2.3 A resolution: specific interactions at subunit interfaces.
  Proteins, 46, 206-214.
PDB code: 1ez4
11389729 L.Ramírez-Silva, S.T.Ferreira, T.Nowak, M.Tuena de Gómez-Puyou, and A.Gómez-Puyou (2001).
Dimethylsulfoxide promotes K+-independent activity of pyruvate kinase and the acquisition of the active catalytic conformation.
  Eur J Biochem, 268, 3267-3274.  
10715009 A.Schramm, B.Siebers, B.Tjaden, H.Brinkmann, and R.Hensel (2000).
Pyruvate kinase of the hyperthermophilic crenarchaeote Thermoproteus tenax: physiological role and phylogenetic aspects.
  J Bacteriol, 182, 2001-2009.  
11112519 C.J.Bond, M.S.Jurica, A.Mesecar, and B.L.Stoddard (2000).
Determinants of allosteric activation of yeast pyruvate kinase and identification of novel effectors using computational screening.
  Biochemistry, 39, 15333-15343.  
10940245 D.S.Goodsell, and A.J.Olson (2000).
Structural symmetry and protein function.
  Annu Rev Biophys Biomol Struct, 29, 105-153.  
10679942 W.Kugler, C.Willaschek, C.Holtz, A.Ohlenbusch, P.Laspe, R.Krügener, H.Muirhead, W.Schröter, and M.Lakomek (2000).
Eight novel mutations and consequences on mRNA and protein level in pyruvate kinase-deficient patients with nonspherocytic hemolytic anemia.
  Hum Mutat, 15, 261-272.  
10966577 X.Zhou, F.Alber, G.Folkers, G.H.Gonnet, and G.Chelvanayagam (2000).
An analysis of the helix-to-strand transition between peptides with identical sequence.
  Proteins, 41, 248-256.  
10378272 E.Horjales, M.M.Altamirano, M.L.Calcagno, R.C.Garratt, and G.Oliva (1999).
The allosteric transition of glucosamine-6-phosphate deaminase: the structure of the T state at 2.3 A resolution.
  Structure, 7, 527-537.
PDB code: 1cd5
10499331 S.Viglio, G.Valentini, L.Chiarelli, G.Zanaboni, G.Cetta, and P.Iadarola (1999).
Micellar electrokinetic chromatography as a complementary method to sodium dodecyl sulfate-polyacrylamide gel electrophoresis for studying limited proteolysis of proteins.
  Electrophoresis, 20, 2400-2406.  
9482576 L.Pastore, R.Della Morte, G.Frisso, F.Alfinito, D.Vitale, R.M.Calise, F.Ferraro, A.Zagari, B.Rotoli, and F.Salvatore (1998).
Novel mutations and structural implications in R-type pyruvate kinase-deficient patients from Southern Italy.
  Hum Mutat, 11, 127-134.  
9519410 M.S.Jurica, A.Mesecar, P.J.Heath, W.Shi, T.Nowak, and B.L.Stoddard (1998).
The allosteric regulation of pyruvate kinase by fructose-1,6-bisphosphate.
  Structure, 6, 195-210.
PDB codes: 1a3w 1a3x
9799487 R.H.Friesen, R.J.Castellani, J.C.Lee, and W.Braun (1998).
Allostery in rabbit pyruvate kinase: development of a strategy to elucidate the mechanism.
  Biochemistry, 37, 15266-15276.  
9184162 A.D.Mesecar, and T.Nowak (1997).
Metal-ion-mediated allosteric triggering of yeast pyruvate kinase. 1. A multidimensional kinetic linked-function analysis.
  Biochemistry, 36, 6792-6802.  
9188741 A.V.Efimov (1997).
Structural trees for protein superfamilies.
  Proteins, 28, 241-260.  
  9278152 L.Piubelli, G.Zanetti, and H.R.Bosshard (1997).
Recombinant wild-type and mutant complexes of ferredoxin and ferredoxin:NADP+ reductase studied by isothermal titration calorimetry.
  Biol Chem, 378, 715-718.  
9428713 L.Ramírez-Silva, J.Oria, A.Gómez-Puyou, and M.Tuena de Gómez-Puyou (1997).
The contribution of water to the selectivity of pyruvate kinase for Na+ and K+.
  Eur J Biochem, 250, 583-589.  
8994883 A.Mattevi, M.Rizzi, and M.Bolognesi (1996).
New structures of allosteric proteins revealing remarkable conformational changes.
  Curr Opin Struct Biol, 6, 824-829.  
9000034 W.G.Hol (1996).
The sophisticated masters of the cell.
  Curr Opin Struct Biol, 6, 777-780.  
8586271 J.Nairn, S.Smith, P.J.Allison, D.Rigden, L.A.Fothergill-Gilmore, and N.C.Price (1995).
Cloning and sequencing of a gene encoding pyruvate kinase from Schizosaccharomyces pombe; implications for quaternary structure and regulation of the enzyme.
  FEMS Microbiol Lett, 134, 221-226.  
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.

 

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