PDBsum entry: 2axn

Transferase, hydrolase

PDB id: 2axn

Contents

Protein chain

451 a.a. *

Ligands

F6P

EDT

ADP

Waters ×353

* Residue conservation analysis

PDB id:

2axn

Name:

Transferase, hydrolase

Title:

Crystal structure of the human inducible form 6- phosphofructo-2-kinase/fructose-2,6-bisphosphatase

Structure:

6-phosphofructo-2-kinase/fructose-2,6- biphosphatase 3 (6pf-2-k/fru- 2,6-p2ase brain/placenta-type isozyme) (ipfk-2) [includes: 6- phosphofructo-2-kinase (ec 2.7.1.105). Fructose-2,6-bisphosphatase (ec 3.1.3.46)]. Chain: a. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: pfkfb3. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

2.10Å R-factor: 0.209 R-free: 0.233

Authors:

S.G.Kim,N.P.Manes,M.R.El-Maghrabi,Y.H.Lee

Key ref:

S.G.Kim et al. (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. PubMed id: 16316985 DOI: 10.1074/jbc.M511019200

Date:

05-Sep-05 Release date: 06-Dec-05

Protein chain

Q16875  (F263_HUMAN) -  6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3

Seq: 520 a.a.

Struc: 451 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: E.C.2.7.1.105 - 6-phosphofructo-2-kinase.
• Reaction: ATP + D-fructose 6-phosphate = ADP + beta-D-fructose 2,6-bisphosphate

ATP + D-fructose 6-phosphate (Bound ligand (Het Group name = F6P) corresponds exactly) = ADP (Bound ligand (Het Group name = ADP) corresponds exactly) + beta-D-fructose 2,6-bisphosphate

• Enzyme class 3: E.C.3.1.3.46 - Fructose-2,6-bisphosphate 2-phosphatase.
• 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 (Bound ligand (Het Group name = F6P) corresponds exactly) + phosphate

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 

• Biological process: metabolic process (3 terms)
• Biochemical function: catalytic activity (10 terms)

reference

DOI no: 10.1074/jbc.M511019200

J Biol Chem 281:2939-2944 (2006)

PubMed id: 16316985

Crystal structure of the hypoxia-inducible form of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase (PFKFB3): a possible new target for cancer therapy.

S.G.Kim, N.P.Manes, M.R.El-Maghrabi, Y.H.Lee.

ABSTRACT

The hypoxia-inducible form of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase (PFKFB3) plays a crucial role in the progression of cancerous cells by enabling their glycolytic pathways even under severe hypoxic conditions. To understand its structural architecture and to provide a molecular scaffold for the design of new cancer therapeutics, the crystal structure of the human form was determined. The structure at 2.1 A resolution shows that the overall folding and functional dimerization are very similar to those of the liver (PFKFB1) and testis (PFKFB4) forms, as expected from sequence homology. However, in this structure, the N-terminal regulatory domain is revealed for the first time among the PFKFB isoforms. With a beta-hairpin structure, the N terminus interacts with the 2-Pase domain to secure binding of fructose-6-phosphate to the active pocket, slowing down the release of fructose-6-phosphate from the phosphoenzyme intermediate product complex. The C-terminal regulatory domain is mostly disordered, leaving the active pocket of the fructose-2,6-bisphosphatase domain wide open. The active pocket of the 6-phosphofructo-2-kinase domain has a more rigid conformation, allowing independent bindings of substrates, fructose-6-phosphate and ATP, with higher affinities than other isoforms. Intriguingly, the structure shows an EDTA molecule bound to the fructose-6-phosphate site of the 6-phosphofructo-2-kinase active pocket despite its unfavorable liganding concentration, suggesting a high affinity. EDTA is not removable from the site with fructose-6-P alone but is with both ATP and fructose-6-P or with fructose-2,6-bisphosphate. This finding suggests that a molecule in which EDTA is covalently linked to ADP is a good starting molecule for the development of new cancer-therapeutic molecules.

Selected figure(s)

Figure 1.
Overall folding of PFKFB3 and the N terminus. A, a ribbon diagram of the dimeric PFKFB3 structure is shown with the bound ligands. One protein subunit is light colored for convenient comparison. ADP are bound to the 2-Kase (magenta) active pocket and Fru-6-P to the 2-Pase (blue). The N-terminal regulatory domain is shown in green. B, The 2 F[o] - F[c] electron density maps are contoured around the N-terminal hairpin structure at 1.1 σ levels. The structure is from the final model. C, a stereo view of the interactions between the N terminus (green) and the 2-Pase domain (gray). The involved hydrogen bonds and salt bridges are shown as broken lines. Unless specifically mentioned, all structural figures were made using MolScript v2.1.2 (45) and rendered using Raster3D v2.7 (46). The electron density maps are drawn using BobScript v1.4b.

Figure 3.
Interactions between the 2-Kase and the bound ligands. A, the presences of EDTA and Fru-2,6-P[2] are shown from the omit maps. The F[o] - F[c] electron density maps are contoured at 2.5 σ levels, and the ligand structures are from the final models. The map of EDTA is shown at the top and that of Fru-2,6-P[2] at the bottom. B, the interactions between EDTA and the 2-Kase active site residues are shown. To show its relative position, ADP is also shown. C, the interactions between Fru-2,6-P[2] and the 2-Kase active site residues are shown. For comparisons of positions of the bound EDTA and Fru-2,6-P[2], the view points were kept similarly.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 2939-2944) copyright 2006.

Figures were selected by an automated process.