PDBsum entry 1lbl

Lyase

PDB id: 1lbl

Contents

Protein chain

247 a.a. *

Ligands

137

Waters ×203

* Residue conservation analysis

PDB id:

1lbl

Name:

Lyase

Title:

Crystal structure of indole-3-glycerol phosphate synthase (igps) in complex with 1-(o-carboxyphenylamino)-1-deoxyribulose 5'-phosphate (cdrp)

Structure:

Indole-3-glycerol phosphate synthase. Chain: a. Engineered: yes

Source:

Sulfolobus solfataricus. Organism_taxid: 2287. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.40Å R-factor: 0.197 R-free: 0.247

Authors:

M.Hennig,B.D.Darimont,K.Kirschner,J.N.Jansonius

Key ref:

M.Hennig et al. (2002). The catalytic mechanism of indole-3-glycerol phosphate synthase: crystal structures of complexes of the enzyme from Sulfolobus solfataricus with substrate analogue, substrate, and product. J Mol Biol, 319, 757-766. PubMed id: 12054868 DOI: 10.1016/S0022-2836(02)00378-9

Date:

04-Apr-02 Release date: 18-Sep-02

Protein chain

Q06121  (TRPC_SULSO) -  Indole-3-glycerol phosphate synthase from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

Seq: 248 a.a.

Struc: 247 a.a.

Enzyme reactions

• Enzyme class: E.C.4.1.1.48 - indole-3-glycerol-phosphate synthase.
• Pathway: Tryptophan Biosynthesis
• Reaction: 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate + H⁺ = (1S,2R)- 1-C-(indol-3-yl)glycerol 3-phosphate + CO2 + H2O

1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate (Bound ligand (Het Group name = 137) corresponds exactly) + H(+) = (1S,2R)- 1-C-(indol-3-yl)glycerol 3-phosphate + CO2 + H2O

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

reference

DOI no: 10.1016/S0022-2836(02)00378-9

J Mol Biol 319:757-766 (2002)

PubMed id: 12054868

The catalytic mechanism of indole-3-glycerol phosphate synthase: crystal structures of complexes of the enzyme from Sulfolobus solfataricus with substrate analogue, substrate, and product.

M.Hennig, B.D.Darimont, J.N.Jansonius, K.Kirschner.

ABSTRACT

Indoleglycerol phosphate synthase catalyzes the ring closure of an N-alkylated anthranilate to a 3-alkyl indole derivative, a reaction requiring Lewis acid catalysis in vitro. Here, we investigated the enzymatic reaction mechanism through X-ray crystallography of complexes of the hyperthermostable enzyme from Sulfolobus solfataricus with the substrate 1-(o-carboxyphenylamino) 1-deoxyribulose 5-phosphate, a substrate analogue and the product indole-3-glycerol phosphate. The substrate and the substrate analogue are bound to the active site in a similar, extended conformation between the previously identified phosphate binding site and a hydrophobic pocket for the anthranilate moiety. This binding mode is unproductive, because the carbon atoms that are to be joined are too far apart. The indole ring of the bound product resides in a second hydrophobic pocket adjacent to that of the anthranilate moiety of the substrate. Although the hydrophobic moiety of the substrate moves during catalysis from one hydrophobic pocket to the other, the triosephosphate moiety remains rigidly bound to the same set of hydrogen-bonding residues. Simultaneously, the catalytically important residues Lys53, Lys110 and Glu159 maintain favourable distances to the atoms of the ligand undergoing covalent changes. On the basis of these data, the structures of two putative catalytic intermediates were modelled into the active site. This new structural information and the modelling studies provide further insight into the mechanism of enzyme-catalyzed indole synthesis. The charged epsilon-amino group of Lys110 is the general acid, and the carboxylate group of Glu159 is the general base. Lys53 guides the substrate undergoing conformational transitions during catalysis, by forming a salt-bridge to the carboxylate group of its anthranilate moiety.

Selected figure(s)

Figure 4.
Figure 4. Stereoview of the difference electron density of the ligands bound to sIGPS, as it appears in electron density omit maps. These were computed with phases resulting from refinement, in which the ligand was omitted. The ligands are shown in a ball-and-stick representation with carbon, oxygen, nitrogen and phosphorus coloured white, red, blue and magenta, respectively, (a) rCdRP on a 2.05 Å map, contoured at 4s. (b) IGP on a 2.0 Å map, contoured at 4s. (c) CdRP and IGP on a 2.4 Å map, contoured at 2.5s. The Figure was produced with MOLOC.[29.]

Figure 6.
Figure 6. The proposed roles of K53, K110 and E159 of sIGPS in catalyzing the conversion of CdRP to IGP. Hydrogen bond distances are given in Table 3. (*) Asymmetric carbon atoms generated transiently. The arrows show how the reactions are assisted by the indicated catalytic residues. See the text for details. (a) The substrate bound unproductively as observed in the sIGPS:CdRP complex ( Figure 3(c)), with C1-C2' DISTANCE=4.8 Å. (b) The intermediate I1 as in Figure 5(a). (c) The intermediate I2 as in Figure 5(b). (d) The sIGPS:IGP complex as in Figure 3(b).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 319, 757-766) copyright 2002.

Figures were selected by the author.