X-ray Structure of MalY from Escherichia Coli: a Pyridoxal 5'-phosphate-dependent Enzyme Acting As a Modulator in Mal Gene Expression

Overview

Journal EMBO J

Specialties Biotechnology
Molecular Biology

Date 2000 Mar 4

PMID 10698925

Citations 14

Authors

T Clausen

A Schlegel

R Peist

E Schneider

C Steegborn

Y S Chang

A Haase

G P Bourenkov

H D Bartunik

W Boos

Affiliations

Soon will be listed here.

Abstract

MalY represents a bifunctional pyridoxal 5'-phosphate-dependent enzyme acting as a beta-cystathionase and as a repressor of the maltose regulon. Here we present the crystal structures of wild-type and A221V mutant protein. Each subunit of the MalY dimer is composed of a large pyridoxal 5'-phosphate-binding domain and a small domain similar to aminotransferases. The structural alignment with related enzymes identifies residues that are generally responsible for beta-lyase activity and depicts a unique binding mode of the pyridoxal 5'-phosphate correlated with a larger, more flexible substrate-binding pocket. In a screen for MalY mutants with reduced mal repressor properties, mutations occurred in three clusters: I, 83-84; II, 181-189 and III, 215-221, which constitute a clearly distinguished region in the MalY crystal structure far away from the cofactor. The tertiary structure of one of these mutants (A221V) demonstrates that positional rearrangements are indeed restricted to regions I, II and III. Therefore, we propose that a direct protein-protein interaction with MalT, the central transcriptional activator of the maltose system, underlies MalY-dependent repression of the maltose system.

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References

Schreiber V, Richet E . Self-association of the Escherichia coli transcription activator MalT in the presence of maltotriose and ATP. J Biol Chem. 1999; 274(47):33220-6. DOI: 10.1074/jbc.274.47.33220. View

Clausen T, Huber R, Laber B, Pohlenz H, Messerschmidt A . Crystal structure of the pyridoxal-5'-phosphate dependent cystathionine beta-lyase from Escherichia coli at 1.83 A. J Mol Biol. 1996; 262(2):202-24. DOI: 10.1006/jmbi.1996.0508. View

Decker K, Gerhardt F, Boos W . The role of the trehalose system in regulating the maltose regulon of Escherichia coli. Mol Microbiol. 1999; 32(4):777-88. DOI: 10.1046/j.1365-2958.1999.01395.x. View

Goldberg J, Swanson R, GOODMAN H, KIRSCH J . The tyrosine-225 to phenylalanine mutation of Escherichia coli aspartate aminotransferase results in an alkaline transition in the spectrophotometric and kinetic pKa values and reduced values of both kcat and Km. Biochemistry. 1991; 30(1):305-12. DOI: 10.1021/bi00215a041. View

Schaaper R . Mechanisms of mutagenesis in the Escherichia coli mutator mutD5: role of DNA mismatch repair. Proc Natl Acad Sci U S A. 1988; 85(21):8126-30. PMC: 282368. DOI: 10.1073/pnas.85.21.8126. View

Schreiber V, Steegborn C, Clausen T, Boos W, Richet E . A new mechanism for the control of a prokaryotic transcriptional regulator: antagonistic binding of positive and negative effectors. Mol Microbiol. 2000; 35(4):765-76. DOI: 10.1046/j.1365-2958.2000.01747.x. View

Mehta P, Christen P . Homology of pyridoxal-5'-phosphate-dependent aminotransferases with the cobC (cobalamin synthesis), nifS (nitrogen fixation), pabC (p-aminobenzoate synthesis) and malY (abolishing endogenous induction of the maltose system) gene products. Eur J Biochem. 1993; 211(1-2):373-6. DOI: 10.1111/j.1432-1033.1993.tb19907.x. View

Debarbouille M, Shuman H, Silhavy T, Schwartz M . Dominant constitutive mutations in malT, the positive regulator gene of the maltose regulon in Escherichia coli. J Mol Biol. 1978; 124(2):359-71. DOI: 10.1016/0022-2836(78)90304-2. View

Bouma C, Roseman S . Sugar transport by the marine chitinolytic bacterium Vibrio furnissii. Molecular cloning and analysis of the glucose and N-acetylglucosamine permeases. J Biol Chem. 1996; 271(52):33457-67. DOI: 10.1074/jbc.271.52.33457. View

10.

ALEXANDER F, Sandmeier E, Mehta P, Christen P . Evolutionary relationships among pyridoxal-5'-phosphate-dependent enzymes. Regio-specific alpha, beta and gamma families. Eur J Biochem. 1994; 219(3):953-60. DOI: 10.1111/j.1432-1033.1994.tb18577.x. View

11.

Rossol I, Puhler A . The Corynebacterium glutamicum aecD gene encodes a C-S lyase with alpha, beta-elimination activity that degrades aminoethylcysteine. J Bacteriol. 1992; 174(9):2968-77. PMC: 205951. DOI: 10.1128/jb.174.9.2968-2977.1992. View

12.

Hayashi H, Mizuguchi H, KAGAMIYAMA H . The imine-pyridine torsion of the pyridoxal 5'-phosphate Schiff base of aspartate aminotransferase lowers its pKa in the unliganded enzyme and is crucial for the successive increase in the pKa during catalysis. Biochemistry. 1998; 37(43):15076-85. DOI: 10.1021/bi981517e. View

13.

Kabsch W, Sander C . Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 1983; 22(12):2577-637. DOI: 10.1002/bip.360221211. View

14.

Yano T, Mizuno T, KAGAMIYAMA H . A hydrogen-bonding network modulating enzyme function: asparagine-194 and tyrosine-225 of Escherichia coli aspartate aminotransferase. Biochemistry. 1993; 32(7):1810-5. DOI: 10.1021/bi00058a015. View

15.

Jones T, Zou J, Cowan S, Kjeldgaard M . Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A. 1991; 47 ( Pt 2):110-9. DOI: 10.1107/s0108767390010224. View

16.

Rhee S, Silva M, Hyde C, Rogers P, Metzler C, Metzler D . Refinement and comparisons of the crystal structures of pig cytosolic aspartate aminotransferase and its complex with 2-methylaspartate. J Biol Chem. 1997; 272(28):17293-302. View

17.

Jansonius J . Structure, evolution and action of vitamin B6-dependent enzymes. Curr Opin Struct Biol. 1999; 8(6):759-69. DOI: 10.1016/s0959-440x(98)80096-1. View

18.

Raibaud O, Richet E . A complex nucleoprotein structure involved in activation of transcription of two divergent Escherichia coli promoters. J Mol Biol. 1989; 205(3):471-85. DOI: 10.1016/0022-2836(89)90218-0. View

19.

Evans S . SETOR: hardware-lighted three-dimensional solid model representations of macromolecules. J Mol Graph. 1993; 11(2):134-8, 127-8. DOI: 10.1016/0263-7855(93)87009-t. View

20.

Holm L, Sander C . Protein structure comparison by alignment of distance matrices. J Mol Biol. 1993; 233(1):123-38. DOI: 10.1006/jmbi.1993.1489. View