PDBsum entry 1w3t

Lyase

PDB id: 1w3t

Contents

Protein chains

293 a.a. *

Ligands

RSH-PYR-3GR ×4

GOL ×4

Waters ×819

* Residue conservation analysis

PDB id:

1w3t

Name:

Lyase

Title:

Sulfolobus solfataricus 2-keto-3-deoxygluconate (kdg) aldolase complex with d-kdgal, d-glyceraldehyde and pyruvate

Structure:

2-keto-3-deoxy gluconate aldolase. Chain: a, b, c, d. Synonym: eda. Engineered: yes

Source:

Sulfolobus solfataricus. Organism_taxid: 2287. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Tetramer (from PDB file)

Resolution:

2.10Å R-factor: 0.155 R-free: 0.204

Authors:

A.Theodossis,H.Walden,E.J.Westwick,H.Connaris,H.J.Lamble,D.W.Hough, M.J.Danson,G.L.Taylor

Key ref:

A.Theodossis et al. (2004). The structural basis for substrate promiscuity in 2-keto-3-deoxygluconate aldolase from the Entner-Doudoroff pathway in Sulfolobus solfataricus. J Biol Chem, 279, 43886-43892. PubMed id: 15265860 DOI: 10.1074/jbc.M407702200

Date:

19-Jul-04 Release date: 02-Sep-04

Protein chains

O54288  (KDGA_SACSO) -  2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase from Saccharolobus solfataricus

Seq: 294 a.a.

Struc: 293 a.a.

Enzyme reactions

• Enzyme class: E.C.4.1.2.55 - 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate
• Reaction:
  1. 2-dehydro-3-deoxy-6-phospho-D-gluconate = D-glyceraldehyde 3-phosphate + pyruvate
  2. 2-dehydro-3-deoxy-6-phospho-D-galactonate = D-glyceraldehyde 3-phosphate + pyruvate

2-dehydro-3-deoxy-6-phospho-D-gluconate (Bound ligand (Het Group name = RSH) matches with 68.75% similarity) = D-glyceraldehyde 3-phosphate + pyruvate

2-dehydro-3-deoxy-6-phospho-D-galactonate = D-glyceraldehyde 3-phosphate + pyruvate (Bound ligand (Het Group name = RSH) matches with 41.67% similarity)

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

reference

DOI no: 10.1074/jbc.M407702200

J Biol Chem 279:43886-43892 (2004)

PubMed id: 15265860

The structural basis for substrate promiscuity in 2-keto-3-deoxygluconate aldolase from the Entner-Doudoroff pathway in Sulfolobus solfataricus.

A.Theodossis, H.Walden, E.J.Westwick, H.Connaris, H.J.Lamble, D.W.Hough, M.J.Danson, G.L.Taylor.

ABSTRACT

The hyperthermophilic Archaea Sulfolobus solfataricus grows optimally above 80 degrees C and metabolizes glucose by a non-phosphorylative variant of the Entner-Doudoroff pathway. In this pathway glucose dehydrogenase and gluconate dehydratase catalyze the oxidation of glucose to gluconate and the subsequent dehydration of gluconate to D-2-keto-3-deoxygluconate (KDG). KDG aldolase (KDGA) then catalyzes the cleavage of KDG to D-glyceraldehyde and pyruvate. It has recently been shown that all the enzymes of this pathway exhibit a catalytic promiscuity that also enables them to be used for the metabolism of galactose. This phenomenon, known as metabolic pathway promiscuity, depends crucially on the ability of KDGA to cleave KDG and D-2-keto-3-deoxygalactonate (KDGal), in both cases producing pyruvate and D-glyceraldehyde. In turn, the aldolase exhibits a remarkable lack of stereoselectivity in the condensation reaction of pyruvate and D-glyceraldehyde, forming a mixture of KDG and KDGal. We now report the structure of KDGA, determined by multiwavelength anomalous diffraction phasing, and confirm that it is a member of the tetrameric N-acetylneuraminate lyase superfamily of Schiff base-forming aldolases. Furthermore, by soaking crystals of the aldolase at more than 80 degrees C below its temperature activity optimum, we have been able to trap Schiff base complexes of the natural substrates pyruvate, KDG, KDGal, and pyruvate plus D-glyceraldehyde, which have allowed rationalization of the structural basis of promiscuous substrate recognition and catalysis. It is proposed that the active site of the enzyme is rigid to keep its thermostability but incorporates extra functionality to be promiscuous.

Selected figure(s)

Figure 3.
FIG. 3. S. solfataricus KGDA catalytic mechanism. Suggested mechanism of KDGA based on that proposed for NAL, indicating the ability of the enzyme to accept substrates that vary at both stereocenters C-4 and C-5. Complexes trapped in this study are shown in bold.

Figure 4.
FIG. 4. Substrate-enzyme interactions. Schematic summary of interactions made with the diastereomers KDG and KDGal.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 43886-43892) copyright 2004.

Figures were selected by the author.