PDBsum entry 2vgf

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Transferase PDB id
Protein chains
517 a.a. *
491 a.a. *
FBP ×4
PGA ×4
_MN ×4
__K ×4
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Human erythrocyte pyruvate kinase: t384m mutant
Structure: Pyruvate kinase isozymes r/l. Chain: a, b, c, d. Fragment: residues 47-574. Synonym: r-type/l-type pyruvate kinase, red cell/liver pyru kinase, pyruvate kinase 1, pyruvate kinase. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 511693.
2.75Å     R-factor:   0.269     R-free:   0.303
Authors: G.Valentini,L.R.Chiarelli,R.Fortin,M.Dolzan,A.Galizzi,D.J.Ab C.Wang,P.Bianchi,A.Zanella,A.Mattevi
Key ref:
G.Valentini et al. (2002). Structure and function of human erythrocyte pyruvate kinase. Molecular basis of nonspherocytic hemolytic anemia. J Biol Chem, 277, 23807-23814. PubMed id: 11960989 DOI: 10.1074/jbc.M202107200
12-Nov-07     Release date:   20-Nov-07    
Supersedes: 1liw
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P30613  (KPYR_HUMAN) -  Pyruvate kinase PKLR
574 a.a.
517 a.a.*
Protein chains
Pfam   ArchSchema ?
P30613  (KPYR_HUMAN) -  Pyruvate kinase PKLR
574 a.a.
491 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.  - Pyruvate kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + pyruvate = ADP + phosphoenolpyruvate
Bound ligand (Het Group name = PGA)
matches with 50.00% similarity
Bound ligand (Het Group name = FBP)
matches with 42.86% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular vesicular exosome   2 terms 
  Biological process     metabolic process   22 terms 
  Biochemical function     catalytic activity     9 terms  


DOI no: 10.1074/jbc.M202107200 J Biol Chem 277:23807-23814 (2002)
PubMed id: 11960989  
Structure and function of human erythrocyte pyruvate kinase. Molecular basis of nonspherocytic hemolytic anemia.
G.Valentini, L.R.Chiarelli, R.Fortin, M.Dolzan, A.Galizzi, D.J.Abraham, C.Wang, P.Bianchi, A.Zanella, A.Mattevi.
Deficiency of human erythrocyte isozyme (RPK) is, together with glucose-6-phosphate dehydrogenase deficiency, the most common cause of the nonspherocytic hemolytic anemia. To provide a molecular framework to the disease, we have solved the 2.7 A resolution crystal structure of human RPK in complex with fructose 1,6-bisphosphate, the allosteric activator, and phosphoglycolate, a substrate analogue, and we have functionally and structurally characterized eight mutants (G332S, G364D, T384M, D390N, R479H, R486W, R504L, and R532W) found in RPK-deficient patients. The mutations target distinct regions of RPK structure, including domain interfaces and catalytic and allosteric sites. The mutations affect to a different extent thermostability, catalytic efficiency, and regulatory properties. These studies are the first to correlate the clinical symptoms with the molecular properties of the mutant enzymes. Mutations greatly impairing thermostability and/or activity are associated with severe anemia. Some mutant proteins exhibit moderate changes in the kinetic parameters, which are sufficient to cause mild to severe anemia, underlining the crucial role of RPK for erythrocyte metabolism. Prediction of the effects of mutations is difficult because there is no relation between the nature and location of the replaced amino acid and the type of molecular perturbation. Characterization of mutant proteins may serve as a valuable tool to assist with diagnosis and genetic counseling.
  Selected figure(s)  
Figure 2.
Fig. 2. The allosteric and catalytic sites of RPK. A, stereo view of the active site with bound phosphoglycolate (indicated by gray bonds), Mn2+, and K+. With respect to Fig. 1A, the model has been rotated by ~30° around an axis horizontal to the plane of the paper. B, stereo view of the allosteric site with bound FBP (gray bonds). The orientation is as in Fig. 1A.
Figure 4.
Fig. 4. The A/C interface in the region surrounding Arg486. The orientation is as in Fig. 1A. A, stereo diagram of the wild-type structure. B, stereo diagram of the R486W mutant structure.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 23807-23814) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20208146 H.P.Morgan, I.W.McNae, K.Y.Hsin, P.A.Michels, L.A.Fothergill-Gilmore, and M.D.Walkinshaw (2010).
An improved strategy for the crystallization of Leishmania mexicana pyruvate kinase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 215-218.
PDB codes: 3is4 3ktx
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
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.  
19320443 A.W.Fenton, and Q.Tang (2009).
An activating interaction between the unphosphorylated n-terminus of human liver pyruvate kinase and the main body of the protein is interrupted by phosphorylation.
  Biochemistry, 48, 3816-3818.  
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.  
17531094 A.Del Sol, M.J.Araúzo-Bravo, D.Amoros, and R.Nussinov (2007).
Modular architecture of protein structures and allosteric communications: potential implications for signaling proteins and regulatory linkages.
  Genome Biol, 8, R92.  
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.  
17547515 N.W.Meza, O.Quintana-Bustamante, A.Puyet, P.Rio, S.Navarro, A.Diez, J.A.Bueren, J.M.Bautista, and J.C.Segovia (2007).
In vitro and in vivo expression of human erythrocyte pyruvate kinase in erythroid cells: a gene therapy approach.
  Hum Gene Ther, 18, 502-514.  
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.  
16704447 S.Pissard, I.Max-Audit, L.Skopinski, A.Vasson, P.Vivien, C.Bimet, M.Goossens, F.Galacteros, and H.Wajcman (2006).
Pyruvate kinase deficiency in France: a 3-year study reveals 27 new mutations.
  Br J Haematol, 133, 683-689.  
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.  
15888079 G.Min-Oo, and P.Gros (2005).
Erythrocyte variants and the nature of their malaria protective effect.
  Cell Microbiol, 7, 753-763.  
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.