PDBsum entry: 1k6m

Transferase, hydrolase

PDB id: 1k6m

Contents

Protein chains

432 a.a. *

Ligands

PO4 ×4

ATG ×2

Waters ×397

* Residue conservation analysis

PDB id:

1k6m

Name:

Transferase, hydrolase

Title:

Crystal structure of human liver 6-phosphofructo-2- kinase/fructose-2,6-bisphosphatase

Structure:

6-phosphofructo-2-kinase/fructose-2,6- biphosphatase 2-phosphatase. Chain: a, b. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PDB file)

Resolution:

2.40Å R-factor: 0.217 R-free: 0.257

Authors:

Y.H.Lee,Y.Li,K.Uyeda,C.A.Hasemann

Key ref:

Y.H.Lee et al. (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. PubMed id: 12379646 DOI: 10.1074/jbc.M209105200

Date:

16-Oct-01 Release date: 11-Dec-02

Protein chains

P16118  (F261_HUMAN) -  6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1

Seq: 471 a.a.

Struc: 432 a.a.*

* PDB and UniProt seqs differ at 5 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 93.00% 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 

• Cellular component: cytosol (2 terms)
• Biological process: metabolic process (18 terms)
• Biochemical function: catalytic activity (12 terms)

reference

DOI no: 10.1074/jbc.M209105200

J Biol Chem 278:523-530 (2003)

PubMed id: 12379646

Tissue-specific structure/function differentiation of the liver isoform of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase.

Y.H.Lee, Y.Li, K.Uyeda, C.A.Hasemann.

ABSTRACT

The crystal structures of the human liver 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase in three different liganding states were determined and compared with those of the rat testis isozyme. A set of amino acid sequence heterogeneity from the two distinct genes encoding the two different tissue isozymes leads to both global and local conformational differences that may cause the differences in catalytic properties of the two isozymes. The sequence differences in a beta-hairpin loop in the kinase domain causes a translational shift of several hydrophobic interactions in the dimeric contact region, and its propagation to the domains interface results in a 5 degrees twist of the entire bisphosphatase domain relative to the kinase domain. The bisphosphatase domain twist allows the dimeric interactions between the bisphosphatase domains, which are negligible in the testis enzyme, and as a result, the conformational stability of the domain is increased. Sequence polymorphisms also confer small but significant structural dissimilarities in the substrate-binding loops, allowing the differentiated catalytic properties between the two different tissue-type isozymes. Whereas the polymorphic sequence at the bisphosphatase-active pocket suggests a more suitable substrate binding, a similar extent of sequence differences at the kinase-active pocket confers a different mechanism of substrates bindings to the kinase-active pocket. It includes the ATP-sensitive unwinding of the switch helix alpha5, which is a characteristic ATP-dependent conformational change in the testis form. The sequence-dependent structural difference disallows the liver kinase to follow the ATP-switch mechanism. Altogether these suggest that the liver isoform has structural features more appropriate for an elevated bisphosphatase activity, compared with that of the testis form. The structural predisposition for bisphosphatase activity in the liver isozyme is consistent with the liver-unique glucose metabolic pathway, gluconeogenesis.

Selected figure(s)

Figure 4.
Fig. 4. Distribution of the temperature (B-) factors in the two isozymes. The C[ ]atom B-factors of the structures of the two isoforms in the same liganding state are compared with each other. The B-factors are expressed as standard deviations from the average values of each structure: dark line, the liver form; gray, the testis form. The functional roles of the protein motifs are labeled above the plots. The motifs used as crystal contacts are underlined as follows: solid line, the liver form; dotted line, the testis form.

Figure 5.
Fig. 5. Sequence-related differences in the substrate loops of the kinase domain. a, ATP-induced switch motion in the liver isozyme. The 5 helix of the liver form (blue) is compared with that of the testis form (gray). The dotted lines demonstrate the additional sequence-related interactions unique in the liver isoform stabilizing the ATP switch: dark dots, hydrogen bonds; green dots, hydrophobic interactions. b, conformation of the 5 helix upon bindings of ADP or P[i]. Note that Lys-174 of testis form (gray) swings out from the bound P[i], and the same result is shown in the ADP complex (data not shown). c, lost coupling between the substrate loops in the liver kinase domain. The sequence difference at C183R causes a loss of hydrogen bonds in the liver form, which serve to couple the two substrate loops in the testis form. The ATP and Fru-6-P loops of the liver enzyme are colored magenta and blue, respectively, whereas the testis loops are in gray. The hydrogen bonds in the testis isozyme are shown with dark dotted lines.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 523-530) copyright 2003.

Figures were selected by an automated process.