spacer
spacer

PDBsum entry 1rd5

Go to PDB code: 
Top Page protein ligands Protein-protein interface(s) links
Lyase PDB id
1rd5
Jmol
Contents
Protein chains
261 a.a.
248 a.a.
Ligands
MLA ×2
Waters ×248

References listed in PDB file
Key reference
Title On the structural basis of the catalytic mechanism and the regulation of the alpha subunit of tryptophan synthase from salmonella typhimurium and bx1 from maize, Two evolutionarily related enzymes.
Authors V.Kulik, E.Hartmann, M.Weyand, M.Frey, A.Gierl, D.Niks, M.F.Dunn, I.Schlichting.
Ref. J Mol Biol, 2005, 352, 608-620. [DOI no: 10.1016/j.jmb.2005.07.014]
PubMed id 16120446
Abstract
Indole is a reaction intermediate in at least two biosynthetic pathways in maize seedlings. In the primary metabolism, the alpha-subunit (TSA) of the bifunctional tryptophan synthase (TRPS) catalyzes the cleavage of indole 3-glycerol phosphate (IGP) to indole and d-glyceraldehyde 3-phosphate (G3P). Subsequently, indole diffuses through the connecting tunnel to the beta-active site where it is condensed with serine to form tryptophan and water. The maize enzyme, BX1, a homolog of TSA, also cleaves IGP to G3P and indole, and the indole is further converted to 2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one, a secondary plant metabolite. BX1 cleaves IGP significantly faster to G3P and indole than does TSA. In line with their different biological functions, these two evolutionary related enzymes differ significantly in their regulatory aspects while catalyzing the same chemistry. Here, the mechanism of IGP cleavage by TSA was analyzed using a novel transition state analogue generated in situ by reaction of 2-aminophenol and G3P. The crystal structure of the complex shows an sp3-hybridized atom corresponding to the C3 position of IGP. The catalytic alphaGlu49 rotates to interact with the sp3-hybridized atom and the 3' hydroxyl group suggesting that it serves both as proton donor and acceptor in the alpha-reaction. The second catalytic residue, alphaAsp60 interacts with the atom corresponding to the indolyl nitrogen, and the catalytically important loop alphaL6 is in the closed, high activity conformation. Comparison of the TSA and TSA-transition state analogue structures with the crystal structure of BX1 suggests that the faster catalytic rate of BX1 may be due to a stabilization of the active conformation: loop alphaL6 is closed and the catalytic glutamate is in the active conformation. The latter is caused by a substitution of the residues that stabilize the inactive conformation in TRPS.
Figure 6.
Figure 6. Environment of the catalytic glutamate. (a) In TPRS, aGlu49 has two conformations, an extended active one interacting with the 3'-hydroxyl of IGP and an inactive one with the carboxylate hydrogen bonded with aTyr173. (b) In BX1 (yellow), Glu134 is positioned in the active conformation. Due to a number of substitutions, including Phe253<->aTyr173 and Ile207<->aLeu127, the corresponding inactive conformation seen in TPRS is not energetically favorable in the BX1 structure.
Figure 7.
Figure 7. The conformation of loop aL6 is determined by the position of an arginine residue. (a) In a-TRPS, the guanidinium group of aArg179 lies in the plane of the loop and forms a number of radial interactions. (b) In BX1 the corresponding guanidinium group, Arg266, is tilted out of the ring plane, resulting in only one interaction with the loop. The two guanidinium groups occupy similar positions in space.
The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 352, 608-620) copyright 2005.
Secondary reference #1
Title Analysis of a chemical plant defense mechanism in grasses.
Authors M.Frey, P.Chomet, E.Glawischnig, C.Stettner, S.Grün, A.Winklmair, W.Eisenreich, A.Bacher, R.B.Meeley, S.P.Briggs, K.Simcox, A.Gierl.
Ref. Science, 1997, 277, 696-699. [DOI no: 10.1126/science.277.5326.696]
PubMed id 9235894
Full text Abstract
Figure 1.
Fig. 1. Structure and chromosomal location of the Bx genes. (A) Schematic representation of the Bx gene cluster on chromosome^ 4. Genetic distances are indicated (in centimorgans). (B) Exon-intron structure of Bx1 through Bx5. Exons are represented^ by boxes. Translation start and stop codons and polyadenylate^ addition sites are shown. Arrows represent insertion of a Mu element in the bx1::Mu and bx3::Mu alleles. The deletion in the bx1 standard^ allele is indicated; it comprises nucleotides 1366 to 2289 of^ the published sequence (9). The distance from Bx1 to Bx2 (2490^ bp) is not drawn to scale. The complete sequences of the genes have been deposited in the European Molecular Biology Laboratory data bank [accession numbers X76713 (Bx1), Y11368 (Bx2), Y11404 (Bx3), X81828 (Bx4), and Y11403 (Bx5)]. (C) Insertion sites of Mu in bx1::Mu and bx3::Mu. The characteristic^ 9-bp host sequence duplication associated with Mu insertion is underlined with an arrow. The insertion occurred at position 2826^ of the genomic DNA sequences in bx1::Mu and at position 1260 in bx3::Mu.
Figure 3.
Fig. 3. Biosynthetic pathways to DIMBOA and tryptophan. Names of gene products are indicated for each of the reactions. BX1 represents a tryptophan synthase activity. BX2 through BX5 represent cytochrome^ P-450-dependent monooxygenases of the CYP71C subfamily. The sequence^ of N-hydroxylation and introduction of the methoxy group at C-7^ of DIMBOA has not yet been elucidated.
The above figures are reproduced from the cited reference with permission from the AAAs
PROCHECK
Go to PROCHECK summary
 Headers