1D2F

X-RAY STRUCTURE OF MALY FROM ESCHERICHIA COLI: A PYRIDOXAL-5'-PHOSPHATE-DEPENDENT ENZYME ACTING AS A MODULATOR IN MAL GENE EXPRESSION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

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

(2000) EMBO J. 19: 831-842

  • DOI: 10.1093/emboj/19.5.831

  • PubMed 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 di ...

    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.


    Related Citations: 
    • Maly of Escherichia-Coli Is an Enzyme With the Activity of a Beta-C-S Lyase (Cystathionase).
      Zdych, E.,Peist, R.,Reidl, J.,Boos, W.
      (1995) J.Bacteriol. 177: 5035


    Organizational Affiliation

    Max-Planck-Institut für Biochemie, Abteilung Strukturforschung, D-82152 Martinsried.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MALY PROTEIN
A, B
390Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: malY
Find proteins for P23256 (Escherichia coli (strain K12))
Go to UniProtKB:  P23256
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP

Download SDF File 
Download CCD File 
A, B
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.201 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 57.510α = 90.00
b = 107.190β = 90.00
c = 256.400γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
CCP4data scaling
MOSFLMdata reduction
MLPHAREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1999-09-23 
  • Released Date: 2000-01-12 
  • Deposition Author(s): Clausen, T.

Revision History 

  • Version 1.0: 2000-01-12
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance