PDBsum entry: 1bif

Bifunctional enzyme

PDB id: 1bif

Contents

Protein chain

432 a.a. *

Ligands

PO4 ×2

ATG

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

Protein chain

P25114  (F264_RAT) -  6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4

Seq: 469 a.a.

Struc: 432 a.a.*

* 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.
• Reaction: ATP + D-fructose 6-phosphate = ADP + beta-D-fructose 2,6-bisphosphate

ATP (Bound ligand (Het Group name = ATG) 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.
• 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 

• Biological process: metabolic process (4 terms)
• Biochemical function: catalytic activity (9 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.