PDBsum entry 1d2f

Transferase

PDB id: 1d2f

Contents

Protein chains

361 a.a. *

Ligands

PLP ×2

Waters ×167

* Residue conservation analysis

PDB id:

1d2f

Name:

Transferase

Title:

X-ray structure of maly from escherichia coli: a pyridoxal-5'- phosphate-dependent enzyme acting as a modulator in mal gene expression

Structure:

Maly protein. Chain: a, b. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.50Å R-factor: 0.201 R-free: 0.262

Authors:

T.Clausen

Key ref:

T.Clausen et al. (2000). X-ray structure of MalY from Escherichia coli: a pyridoxal 5'-phosphate-dependent enzyme acting as a modulator in mal gene expression. EMBO J, 19, 831-842. PubMed id: 10698925 DOI: 10.1093/emboj/19.5.831

Date:

23-Sep-99 Release date: 12-Jan-00

Protein chains

P23256  (MALY_ECOLI) -  Protein MalY from Escherichia coli (strain K12)

Seq: 390 a.a.

Struc: 361 a.a.

Enzyme reactions

• Enzyme class: E.C.4.4.1.13 - cysteine-S-conjugate beta-lyase.
• Reaction: an S-substituted L-cysteine + H2O = a thiol + pyruvate + NH4⁺
• Cofactor: Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (Bound ligand (Het Group name = PLP) matches with 93.75% similarity)

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

reference

DOI no: 10.1093/emboj/19.5.831

EMBO J 19:831-842 (2000)

PubMed id: 10698925

X-ray structure of MalY from Escherichia coli: a pyridoxal 5'-phosphate-dependent enzyme acting as a modulator in mal gene expression.

T.Clausen, A.Schlegel, R.Peist, E.Schneider, C.Steegborn, Y.S.Chang, A.Haase, G.P.Bourenkov, H.D.Bartunik, W.Boos.

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.

Selected figure(s)

Figure 4.
Figure 4 MalT-binding site. (A) The active dimer of MalY illustrating the location of the MalT interaction patch. The C^ traces of both monomers (white and green) are overlaid with a transparent surface. The MalT interaction regions are emphasized by a solid surface that was defined on the basis of the negative repressor mutants (drawn in red). The PLP cofactor is shown in a van der Waals representation. Note that the MalT-binding surface and the active site entrance to the PLP cofactor are located on opposite sides of the individual MalY monomers. (B) Spatial structure of the MalT-binding patch, which is constructed from the three segments I, II and III as described in the text. The C atoms of segments I, II and III are coloured orange (residues 81–85), white (residues 179–191) and green (residues 212–222), respectively. For each segment, the most important residue regarding MalT repression (Table II) is labelled. The model is overlaid with a transparent surface that is colour coded by atom type. (C) Overlay of the wild-type and A221V MalT interaction segments I, II and III. The wild-type model and the corresponding surface are in white, the A221V mutant in green. Obviously, the mutation Ala221 to Val221 results in a concerted structural reorientation of all three segments. The orientations of (B) and (C) are identical.

Figure 5.
Figure 5 Active site entrances of MalY (left) and CBL (right). The orientation and scaling of both figures are identical. The corresponding PLP cofactors are shown in a van der Waals representation below the surface. Part of the phosphate group of the MalY cofactor is directly accessible in the active site cleft.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2000, 19, 831-842) copyright 2000.

Figures were selected by an automated process.