PDBsum entry 1ok4

Lyase

PDB id: 1ok4

Contents

Protein chains

(+ 4 more) 251 a.a. *

Ligands

13P ×10

Waters ×641

* Residue conservation analysis

PDB id:

1ok4

Name:

Lyase

Title:

Archaeal fructose 1,6-bisphosphate aldolase covalently bound to the substrate dihydroxyacetone phosphate

Structure:

Fructose-bisphosphate aldolase class i. Chain: a, b, c, d, e, f, g, h, i, j. Synonym: fbp aldolase. Engineered: yes. Other_details: lys177 schiff-base with dhap

Source:

Thermoproteus tenax. Organism_taxid: 2271. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Pentamer (from PDB file)

Resolution:

2.10Å R-factor: 0.164 R-free: 0.185

Authors:

E.Lorentzen,P.Zwart,A.Stark,R.Hensel,B.Siebers,E.Pohl

Key ref:

E.Lorentzen et al. (2003). Crystal structure of an archaeal class I aldolase and the evolution of (betaalpha)8 barrel proteins. J Biol Chem, 278, 47253-47260. PubMed id: 12941964 DOI: 10.1074/jbc.M305922200

Date:

17-Jul-03 Release date: 04-Sep-03

Protein chains

P58315  (ALF1_THETK) -  Fructose-bisphosphate aldolase class 1 from Thermoproteus tenax (strain ATCC 35583 / DSM 2078 / JCM 9277 / NBRC 100435 / Kra 1)

Seq: 263 a.a.

Struc: 251 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

beta-D-fructose 1,6-bisphosphate = D-glyceraldehyde 3-phosphate (Bound ligand (Het Group name = 13P) matches with 90.00% similarity) + dihydroxyacetone phosphate

• Cofactor: Zn(2+)

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

reference

DOI no: 10.1074/jbc.M305922200

J Biol Chem 278:47253-47260 (2003)

PubMed id: 12941964

Crystal structure of an archaeal class I aldolase and the evolution of (betaalpha)8 barrel proteins.

E.Lorentzen, E.Pohl, P.Zwart, A.Stark, R.B.Russell, T.Knura, R.Hensel, B.Siebers.

ABSTRACT

Fructose-1,6-bisphosphate aldolase (FBPA) catalyzes the reversible cleavage of fructose 1,6-bisphosphate to glyceraldehyde 3-phosphate and dihydroxyacetone phosphate in the glycolytic pathway. FBPAs from archaeal organisms have recently been identified and characterized as a divergent family of proteins. Here, we report the first crystal structure of an archaeal FBPA at 1.9-A resolution. The structure of this 280-kDa protein complex was determined using single wavelength anomalous dispersion followed by 10-fold non-crystallographic symmetry averaging and refined to an R-factor of 14.9% (Rfree 17.9%). The protein forms a dimer of pentamers, consisting of subunits adopting the ubiquitous (betaalpha)8 barrel fold. Additionally, a crystal structure of the archaeal FBPA covalently bound to dihydroxyacetone phosphate was solved at 2.1-A resolution. Comparison of the active site residues with those of classical FBPAs, which share no significant sequence identity but display the same overall fold, reveals a common ancestry between these two families of FBPAs. Structural comparisons, furthermore, establish an evolutionary link to the triosephosphate isomerases, a superfamily hitherto considered independent from the superfamily of aldolases.

Selected figure(s)

Figure 1.
FIG. 1. A, ribbon diagram of the crystal structure of the Tt-FBPA decamer. Two pentamers face each other with the N-terminal side of the TIM barrels to form the decamer. Each monomer in the pentamers is shown in different colors and the two pentamers in different shadings. The active sites are located at the C termini of the TIM barrels and point away from the pentamer-pentamer interface. B, one pentamer is shown in a view perpendicular to that of A, using the same color coding.

Figure 3.
FIG. 3. Close-up of the central hole of the pentamer in the same orientation and color coding as Fig. 1B. The residues Phe-119, Trp-121, and Lys-122 from each monomer, shown in ball-and-stick representation, point into the central hole of the pentamer and perform a continuous stacking.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 47253-47260) copyright 2003.

Figures were selected by an automated process.