spacer
spacer

PDBsum entry 1bif

Go to PDB code: 
protein ligands metals links
Bifunctional enzyme PDB id
1bif
Jmol
Contents
Protein chain
432 a.a. *
Ligands
PO4 ×2
AGS
GOL
Metals
_MG
Waters ×319
* Residue conservation analysis
PDB id:
1bif
Name: Bifunctional enzyme
Title: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase bifunct enzyme complexed with atp-g-s and phosphate
Structure: 6-phosphofructo-2-kinase/ fructose-2,6-bisphospha chain: a. Engineered: yes. Mutation: yes
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116. Cell_line: bl21. Organ: testis. Gene: rt2k. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_cell_line: bl21.
Resolution:
2.00Å     R-factor:   0.183     R-free:   0.250
Authors: C.A.Hasemann,J.Deisenhofer
Key ref:
C.A.Hasemann et al. (1996). The crystal structure of the bifunctional enzyme 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase reveals distinct domain homologies. Structure, 4, 1017-1029. PubMed id: 8805587 DOI: 10.1016/S0969-2126(96)00109-8
Date:
08-Nov-96     Release date:   12-Nov-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P25114  (F264_RAT) -  6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4
Seq:
Struc:
469 a.a.
432 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class 1: E.C.2.7.1.105  - 6-phosphofructo-2-kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + D-fructose 6-phosphate = ADP + beta-D-fructose 2,6-bisphosphate
ATP
Bound ligand (Het Group name = AGS)
matches with 93.75% similarity
+ D-fructose 6-phosphate
= ADP
+ beta-D-fructose 2,6-bisphosphate
   Enzyme class 2: E.C.3.1.3.46  - Fructose-2,6-bisphosphate 2-phosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Beta-D-fructose 2,6-bisphosphate + H2O = D-fructose 6-phosphate + phosphate
Beta-D-fructose 2,6-bisphosphate
+ H(2)O
= D-fructose 6-phosphate
+
phosphate
Bound ligand (Het Group name = PO4)
corresponds exactly
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   6 terms 
  Biochemical function     catalytic activity     8 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(96)00109-8 Structure 4:1017-1029 (1996)
PubMed id: 8805587  
 
 
The crystal structure of the bifunctional enzyme 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase reveals distinct domain homologies.
C.A.Hasemann, E.S.Istvan, K.Uyeda, J.Deisenhofer.
 
  ABSTRACT  
 
BACKGROUND. Glucose homeostasis is maintained by the processes of glycolysis and gluconeogenesis. The importance of these pathways is demonstrated by the severe and life threatening effects observed in various forms of diabetes. The bifunctional enzyme 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase catalyzes both the synthesis and degradation of fructose-2,6-bisphosphate, a potent regulator of glycolysis. Thus this bifunctional enzyme plays an indirect yet key role in the regulation of glucose metabolism. RESULTS. We have determined the 2.0 A crystal structure of the rat testis isozyme of this bifunctional enzyme. The enzyme is a homodimer of 55 kDa subunits arranged in a head-to-head fashion, with each monomer consisting of independent kinase and phosphatase domains. The location of ATPgammaS and inorganic phosphate in the kinase and phosphatase domains, respectively, allow us to locate and describe the active sites of both domains. CONCLUSIONS. The kinase domain is clearly related to the superfamily of mononucleotide binding proteins, with a particularly close relationship to the adenylate kinases and the nucleotide-binding portion of the G proteins. This is in disagreement with the broad speculation that this domain would resemble phosphofructokinase. The phosphatase domain is structurally related to a family of proteins which includes the cofactor independent phosphoglycerate mutases and acid phosphatases.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. Nucleotide-protein interactions of the 6-PF-2-K domain. (a) Stereo view of ATPgS bound in the 6-PF-2-K active site. Close contacts between the ATPgS, Mg2+, Lys172, Lys51, Thr52, and Asp128 are shown as white lines. Also shown are Arg78, Arg79 and Arg193 residues which have been shown to affect F6P binding. The multiple hydrogen bonds formed between the phosphate oxygens and the main chain nitrogens in the loop connecting b1-1 and a1 are not shown. (b) Stereo view of the superposition of the 6-PF-2-K (purple), the G protein G[ia] (orange), and uridylate kinase (UDK) (turquoise) active sites. The G[ia] coordinates are from the AIFI[4]^ - transition state analogue structure [44], and thus include the planar AIFI[4]- moiety shown in yellow. The UDK structure includes two bound ADP molecules, thus representing the ADP-product complex [42]. The structures were superimposed using only the protein coordinates of the ATP-binding loops; this results in an excellent superposition of the 6-PF-2-K g-phosphate, the G[ia] AIFI[4]-, and the UDK product (b-phosphate).
 
  The above figure is reprinted by permission from Cell Press: Structure (1996, 4, 1017-1029) copyright 1996.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20551224 W.Yang, M.Pollard, Y.Li-Beisson, F.Beisson, M.Feig, and J.Ohlrogge (2010).
A distinct type of glycerol-3-phosphate acyltransferase with sn-2 preference and phosphatase activity producing 2-monoacylglycerol.
  Proc Natl Acad Sci U S A, 107, 12040-12045.  
19015259 H.Li, and G.Jogl (2009).
Structural and Biochemical Studies of TIGAR (TP53-induced Glycolysis and Apoptosis Regulator).
  J Biol Chem, 284, 1748-1754.  
17348005 L.Davies, I.P.Anderson, P.C.Turner, A.D.Shirras, H.H.Rees, and D.J.Rigden (2007).
An unsuspected ecdysteroid/steroid phosphatase activity in the key T-cell regulator, Sts-1: surprising relationship to insect ecdysteroid phosphate phosphatase.
  Proteins, 67, 720-731.  
17986204 S.Stingo, M.Masullo, E.Polverini, C.Laezza, I.Ruggiero, R.Arcone, E.Ruozi, F.Dal Piaz, A.M.Malfitano, A.M.D'Ursi, and M.Bifulco (2007).
The N-terminal domain of 2',3'-cyclic nucleotide 3'-phosphodiesterase harbors a GTP/ATP binding site.
  Chem Biol Drug Des, 70, 502-510.  
16316985 S.G.Kim, N.P.Manes, M.R.El-Maghrabi, and Y.H.Lee (2006).
Crystal structure of the hypoxia-inducible form of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase (PFKFB3): a possible new target for cancer therapy.
  J Biol Chem, 281, 2939-2944.
PDB code: 2axn
15670209 K.Hamada, M.Kato, T.Shimizu, K.Ihara, T.Mizuno, and T.Hakoshima (2005).
Crystal structure of the protein histidine phosphatase SixA in the multistep His-Asp phosphorelay.
  Genes Cells, 10, 1.
PDB codes: 1ujb 1ujc
16008555 N.Chevalier, L.Bertrand, M.H.Rider, F.R.Opperdoes, D.J.Rigden, and P.A.Michels (2005).
6-Phosphofructo-2-kinase and fructose-2,6-bisphosphatase in Trypanosomatidae. Molecular characterization, database searches, modelling studies and evolutionary analysis.
  FEBS J, 272, 3542-3560.  
15096219 D.G.Guerra, D.Vertommen, L.A.Fothergill-Gilmore, F.R.Opperdoes, and P.A.Michels (2004).
Characterization of the cofactor-independent phosphoglycerate mutase from Leishmania mexicana mexicana. Histidines that coordinate the two metal ions in the active site show different susceptibilities to irreversible chemical modification.
  Eur J Biochem, 271, 1798-1810.  
14997573 I.L.de La Sierra-Gallay, B.Collinet, M.Graille, S.Quevillon-Cheruel, D.Liger, P.Minard, K.Blondeau, G.Henckes, R.Aufrère, N.Leulliot, C.Z.Zhou, I.Sorel, J.L.Ferrer, A.Poupon, J.Janin, and H.van Tilbeurgh (2004).
Crystal structure of the YGR205w protein from Saccharomyces cerevisiae: close structural resemblance to E. coli pantothenate kinase.
  Proteins, 54, 776-783.
PDB code: 1odf
14754987 J.H.Eastberg, J.Pelletier, and B.L.Stoddard (2004).
Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase.
  Nucleic Acids Res, 32, 653-660.
PDB codes: 1rc8 1rpz 1rrc
15583379 J.H.Pereira, J.S.de Oliveira, F.Canduri, M.V.Dias, M.S.Palma, L.A.Basso, D.S.Santos, and W.F.de Azevedo (2004).
Structure of shikimate kinase from Mycobacterium tuberculosis reveals the binding of shikimic acid.
  Acta Crystallogr D Biol Crystallogr, 60, 2310-2319.
PDB code: 1we2
12414806 B.Singh, and N.B.Schwartz (2003).
Identification and functional characterization of the novel BM-motif in the murine phosphoadenosine phosphosulfate (PAPS) synthetase.
  J Biol Chem, 278, 71-75.  
14579361 R.P.Bahadur, P.Chakrabarti, F.Rodier, and J.Janin (2003).
Dissecting subunit interfaces in homodimeric proteins.
  Proteins, 53, 708-719.  
12379646 Y.H.Lee, Y.Li, K.Uyeda, and C.A.Hasemann (2003).
Tissue-specific structure/function differentiation of the liver isoform of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase.
  J Biol Chem, 278, 523-530.
PDB code: 1k6m
12110598 L.K.Wang, C.D.Lima, and S.Shuman (2002).
Structure and mechanism of T4 polynucleotide kinase: an RNA repair enzyme.
  EMBO J, 21, 3873-3880.
PDB code: 1ly1
12370296 N.Carpino, R.Kobayashi, H.Zang, Y.Takahashi, S.T.Jou, J.Feng, H.Nakajima, and J.N.Ihle (2002).
Identification, cDNA cloning, and targeted deletion of p70, a novel, ubiquitously expressed SH3 domain-containing protein.
  Mol Cell Biol, 22, 7491-7500.  
11165514 D.A.Okar, A.Manzano, A.Navarro-Sabatè, L.Riera, R.Bartrons, and A.J.Lange (2001).
PFK-2/FBPase-2: maker and breaker of the essential biofactor fructose-2,6-bisphosphate.
  Trends Biochem Sci, 26, 30-35.  
11514674 D.J.Rigden, I.Bagyan, E.Lamani, P.Setlow, and M.J.Jedrzejas (2001).
A cofactor-dependent phosphoglycerate mutase homolog from Bacillus stearothermophilus is actually a broad specificity phosphatase.
  Protein Sci, 10, 1835-1846.  
11568503 M.R.El-Maghrabi, F.Noto, N.Wu, and N.Manes (2001).
6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase: suiting structure to need, in a family of tissue-specific enzymes.
  Curr Opin Clin Nutr Metab Care, 4, 411-418.  
11522786 S.Baltrusch, S.Lenzen, D.A.Okar, A.J.Lange, and M.Tiedge (2001).
Characterization of glucokinase-binding protein epitopes by a phage-displayed peptide library. Identification of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase as a novel interaction partner.
  J Biol Chem, 276, 43915-43923.  
11483496 V.Monedero, S.Poncet, I.Mijakovic, S.Fieulaine, V.Dossonnet, I.Martin-Verstraete, S.Nessler, and J.Deutscher (2001).
Mutations lowering the phosphatase activity of HPr kinase/phosphatase switch off carbon metabolism.
  EMBO J, 20, 3928-3937.  
10933792 D.A.Okar, D.H.Live, M.H.Devany, and A.J.Lange (2000).
Mechanism of the bisphosphatase reaction of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase probed by (1)H-(15)N NMR spectroscopy.
  Biochemistry, 39, 9754-9762.  
11106417 J.Nairn, D.Duncan, N.E.Price, S.M.Kelly, L.A.Fothergill-Gilmore, S.Uhrinova, P.N.Barlow, D.J.Rigden, and N.C.Price (2000).
Characterization of active-site mutants of Schizosaccharomyces pombe phosphoglycerate mutase. Elucidation of the roles of amino acids involved in substrate binding and catalysis.
  Eur J Biochem, 267, 7065-7074.  
11123954 M.Sakurai, P.F.Cook, C.A.Haseman, and K.Uyeda (2000).
Glutamate 325 is a general acid-base catalyst in the reaction catalyzed by fructose-2,6-bisphosphatase.
  Biochemistry, 39, 16238-16243.  
11209754 Z.Zhu, S.Ling, Q.H.Yang, and L.Li (2000).
The difference in the carboxy-terminal sequence is responsible for the difference in the activity of chicken and rat liver fructose-2,6-bisphosphatase.
  Biol Chem, 381, 1195-1202.  
  10475585 D.A.Okar, and A.J.Lange (1999).
Fructose-2,6-bisphosphate and control of carbohydrate metabolism in eukaryotes.
  Biofactors, 10, 1.  
10194369 D.A.Okar, D.H.Live, T.L.Kirby, E.J.Karschnia, L.B.von Weymarn, I.M.Armitage, and A.J.Lange (1999).
The roles of Glu-327 and His-446 in the bisphosphatase reaction of rat liver 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase probed by NMR spectroscopic and mutational analyses of the enzyme in the transient phosphohistidine intermediate complex.
  Biochemistry, 38, 4471-4479.  
9890979 H.Mizuguchi, P.F.Cook, C.H.Tai, C.A.Hasemann, and K.Uyeda (1999).
Reaction mechanism of fructose-2,6-bisphosphatase. A mutation of nucleophilic catalyst, histidine 256, induces an alteration in the reaction pathway.
  J Biol Chem, 274, 2166-2175.  
9890980 M.H.Yuen, H.Mizuguchi, Y.H.Lee, P.F.Cook, K.Uyeda, and C.A.Hasemann (1999).
Crystal structure of the H256A mutant of rat testis fructose-6-phosphate,2-kinase/fructose-2,6-bisphosphatase. Fructose 6-phosphate in the active site leads to mechanisms for both mutant and wild type bisphosphatase activities.
  J Biol Chem, 274, 2176-2184.
PDB code: 2bif
9548738 D.H.Harrison, J.A.Runquist, A.Holub, and H.M.Miziorko (1998).
The crystal structure of phosphoribulokinase from Rhodobacter sphaeroides reveals a fold similar to that of adenylate kinase.
  Biochemistry, 37, 5074-5085.
PDB code: 1a7j
9477947 J.A.Runquist, D.H.Harrison, and H.M.Miziorko (1998).
Functional evaluation of invariant arginines situated in the mobile lid domain of phosphoribulokinase.
  Biochemistry, 37, 1221-1226.  
9760241 M.K.Helms, T.L.Hazlett, H.Mizuguchi, C.A.Hasemann, K.Uyeda, and D.M.Jameson (1998).
Site-directed mutants of rat testis fructose 6-phosphate, 2-kinase/fructose 2,6-bisphosphatase: localization of conformational alterations induced by ligand binding.
  Biochemistry, 37, 14057-14064.  
9323207 C.D.Lima, M.G.Klein, and W.A.Hendrickson (1997).
Structure-based analysis of catalysis and substrate definition in the HIT protein family.
  Science, 278, 286-290.
PDB codes: 1av5 1kpe 1kpf 4fit 5fit 6fit
9325256 D.Potter, and H.M.Miziorko (1997).
Identification of catalytic residues in human mevalonate kinase.
  J Biol Chem, 272, 25449-25454.  
9220964 H.Mizuguchi, P.F.Cook, C.A.Hasemann, and K.Uyeda (1997).
Chemical mechanism of the fructose-6-phosphate,2-kinase reaction from the pH dependence of kinetic parameters of site-directed mutants of active site basic residues.
  Biochemistry, 36, 8775-8784.  
9253407 Y.H.Lee, T.W.Olson, C.M.Ogata, D.G.Levitt, L.J.Banaszak, and A.J.Lange (1997).
Crystal structure of a trapped phosphoenzyme during a catalytic reaction.
  Nat Struct Biol, 4, 615-618.
PDB code: 1tip
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.