2V5L

Structures of the Open and Closed State of Trypanosomal Triosephosphate Isomerase: as Observed in a New Crystal Form: Implications for the Reaction Mechanism

Summary for 2V5L

• Entry DOI: 10.2210/pdb2v5l/pdb
• Related: 1AG1 1DKW 1IIG 1IIH 1KV5 1ML1 1MSS 1MTM 1TPD 1TPE 1TPF 1TRD 1TRI 1TSI 1TTI 1TTJ 2J24 2J27 2V0T 2V2C 2V2D 2V2H 3TIM 4TIM 5TIM 6TIM
• Descriptor: TRIOSEPHOSPHATE ISOMERASE, SULFATE ION (3 entities in total)
• Functional Keywords: oxidoreductase, triosephosphate isomerase, pentose shunt, gluconeogenesis, binding studies, tim, isomerase, glycosome, glycolysis, engineering, lipid synthesis, fatty acid biosynthesis
• Biological source: TRYPANOSOMA BRUCEI BRUCEI
• Cellular location: Glycosome: P04789
• Total number of polymer chains: 2
• Total formula weight: 53923.79

Authors

Noble, M.E.M.,Zeelen, J.P.,Wierenga, R.K. (deposition date: 2007-07-06, release date: 2007-07-31, Last modification date: 2024-05-08)

Primary citation

Noble, M.E.M.,Zeelen, J.P.,Wierenga, R.K.
Structures of the Open and Closed State of Trypanosomal Triosephosphate Isomerase: As Observed in a New Crystal Form: Implications for the Reaction Mechanism
Proteins: Struct.,Funct., Genet., 16:311-, 1993

PubMed Abstract: The structure of trypanosomal triosephosphate isomerase (TIM) has been solved at a resolution of 2.1A in a new crystal form grown at pH 8.8 from PEG6000. In this new crystal form (space group C2, cell dimensions 94.8 A, 48.3 A, 131.0 A, 90.0 degrees, 100.3 degrees, 90.0 degrees), TIM is present in a ligand-free state. The asymmetric unit consists of two TIM subunits. Each of these subunits is part of a dimer which is sitting on a crystallographic twofold axis, such that the crystal packing is formed from two TIM dimers in two distinct environments. The two constituent monomers of a given dimer are, therefore, crystallographically equivalent. In the ligand-free state of TIM in this crystal form, the two types of dimer are very similar in structure, with the flexible loops in the "open" conformation. For one dimer (termed molecule-1), the flexible loop (loop-6) is involved in crystal contacts. Crystals of this type have been used in soaking experiments with 0.4 M ammonium sulphate (studied at 2.4 A resolution), and with 40 microM phosphoglycolohydroxamate (studied at 2.5 A resolution). It is found that transfer to 0.4 M ammonium sulphate (equal to 80 times the Ki of sulphate for TIM), gives rise to significant sulphate binding at the active site of one dimer (termed molecule-2), and less significant binding at the active site of the other. In neither dimer does sulphate induce a "closed" conformation. In a mother liquor containing 40 microM phosphoglycolohydroxamate (equal to 10 times the Ki of phosphoglycolohydroxamate for TIM), an inhibitor molecule binds at the active site of only that dimer of which the flexible loop is free from crystal contacts (molecule-2). In this dimer, it induces a closed conformation. These three structures are compared and discussed with respect to the mode of binding of ligand in the active site as well as with respect to the conformational changes resulting from ligand binding.

PubMed: 8356028
DOI: 10.1002/PROT.340160402

Experimental method

X-RAY DIFFRACTION (2.4 Å)