PDBsum entry 1rv8

Lyase

PDB id: 1rv8

Contents

Protein chains

297 a.a. *

Ligands

SO4 ×12

Metals

_CO ×5

_NA ×4

Waters ×932

* Residue conservation analysis

PDB id:

1rv8

Name:

Lyase

Title:

Class ii fructose-1,6-bisphosphate aldolase from thermus aquaticus in complex with cobalt

Structure:

Fructose-1,6-bisphosphate aldolase. Chain: a, b, c, d. Engineered: yes

Source:

Thermus aquaticus. Organism_taxid: 271. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Tetramer (from PQS)

Resolution:

2.30Å R-factor: 0.211 R-free: 0.252

Authors:

T.Izard,J.Sygusch

Key ref:

T.Izard and J.Sygusch (2004). Induced fit movements and metal cofactor selectivity of class II aldolases: structure of Thermus aquaticus fructose-1,6-bisphosphate aldolase. J Biol Chem, 279, 11825-11833. PubMed id: 14699122 DOI: 10.1074/jbc.M311375200

Date:

12-Dec-03 Release date: 27-Jan-04

Protein chains

Q9RHA2  (Q9RHA2_THEAQ) -  Fructose-1,6-bisphosphate aldolase from Thermus aquaticus

Seq: 305 a.a.

Struc: 297 a.a.

Enzyme reactions

• Enzyme class: E.C.4.1.2.13 - fructose-bisphosphate aldolase.
• Reaction: beta-D-fructose 1,6-bisphosphate = D-glyceraldehyde 3-phosphate + dihydroxyacetone phosphate
• Cofactor: Zn(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1074/jbc.M311375200

J Biol Chem 279:11825-11833 (2004)

PubMed id: 14699122

Induced fit movements and metal cofactor selectivity of class II aldolases: structure of Thermus aquaticus fructose-1,6-bisphosphate aldolase.

T.Izard, J.Sygusch.

ABSTRACT

Fructose-1,6-bisphosphate (FBP) aldolase is an essential glycolytic enzyme that reversibly cleaves its ketohexose substrate into triose phosphates. Here we report the crystal structure of a metallo-dependent or class II FBP aldolase from an extreme thermophile, Thermus aquaticus (Taq). The quaternary structure reveals a tetramer composed of two dimers related by a 2-fold axis. Taq FBP aldolase subunits exhibit two distinct conformational states corresponding to loop regions that are in either open or closed position with respect to the active site. Loop closure remodels the disposition of chelating active site histidine residues. In subunits corresponding to the open conformation, the metal cofactor, Co(2+), is sequestered in the active site, whereas for subunits in the closed conformation, the metal cation exchanges between two mutually exclusive binding loci, corresponding to a site at the active site surface and an interior site vicinal to the metal-binding site in the open conformation. Cofactor site exchange is mediated by rotations of the chelating histidine side chains that are coupled to the prior conformational change of loop closure. Sulfate anions are consistent with the location of the phosphate-binding sites of the FBP substrate and determine not only the previously unknown second phosphate-binding site but also provide a mechanism that regulates loop closure during catalysis. Modeling of FBP substrate into the active site is consistent with binding by the acyclic keto form, a minor solution species, and with the metal cofactor mediating keto bond polarization. The Taq FBP aldolase structure suggests a structural basis for different metal cofactor specificity than in Escherichia coli FBP aldolase structures, and we discuss its potential role during catalysis. Comparison with the E. coli structure also indicates a structural basis for thermostability by Taq FBP aldolase.

Selected figure(s)

Figure 2.
FIG. 2. A cartoon drawing of the FBP aldolase oligomer with point group 222. The three different molecular dyads comprise a right-handed orthogonal set of axes P, Q, and R as originally defined for the three 2-fold axes of lactate dehydrogenase (46). In A, the view is looking down the crystallographic dyad (P), while in B the orientation is looking down the molecular dyad (R). The dyads (R and Q in A and P and Q in B) are indicated by solid lines. Each protomer is shown in a different color.

Figure 4.
FIG. 4. Stereo view of Taq FBP aldolase active site. Final [A] weighted F[o] - F[c] omit electron density map for ligands bound to the enzyme. The contour level of the electron density map is 4 , and the resolution is 2.3 Å. The bonds of the ligands are drawn in pink, whereas the bonds of the enzyme are shown in light gray. For clarity, water molecules (drawn as spheres) are not labeled. Residues belonging to a 2-fold related subunit are italicized. A, protomer in the closed conformation showing residues in contact with the sulfate anions that coincide with the phosphate-binding sites of FBP, the two mutually exclusive Co2+ cofactors (drawn as light blue spheres) and the activating cation (drawn as a black sphere). B, sulfate and cation binding to the active site as observed in the subunits in their open conformation. Orientation was rotated by 15° with respect to A to reveal Asn251 that interacts with the monovalent cation. C, FBP modeled into the active site using the sulfate-binding sites of the closed protomer as phosphate oxyanion templates in the Taq FBP aldolase complex with yttrium. The novel metal-binding site (yttrium) is drawn as a green sphere. The hydroxyls O[2] and O[3] of the FBP molecule are within close contact of the exterior Co2+ site (indicated by dashed lines).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 11825-11833) copyright 2004.

Figures were selected by an automated process.