1NVM

Crystal structure of a bifunctional aldolase-dehydrogenase : sequestering a reactive and volatile intermediate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of a bifunctional aldolase-dehydrogenase: Sequestering a reactive and volatile intermediate

Manjasetty, A.B.Powlowski, J.Vrielink, A.

(2003) Proc.Natl.Acad.Sci.USA 100: 6992-6997

  • DOI: 10.1073/pnas.1236794100

  • PubMed Abstract: 
  • The crystal structure of the bifunctional enzyme 4-hydroxy-2-ketovalerate aldolase (DmpG)/acylating acetaldehyde dehydrogenase (DmpF), which is involved in the bacterial degradation of toxic aromatic compounds, has been determined by multiwavelength ...

    The crystal structure of the bifunctional enzyme 4-hydroxy-2-ketovalerate aldolase (DmpG)/acylating acetaldehyde dehydrogenase (DmpF), which is involved in the bacterial degradation of toxic aromatic compounds, has been determined by multiwavelength anomalous dispersion (MAD) techniques and refined to 1.7-A resolution. Structures of the two polypeptides represent a previously unrecognized subclass of metal-dependent aldolases, and of a CoA-dependent dehydrogenase. The structure reveals a mixed state of NAD+ binding to the DmpF protomer. Domain movements associated with cofactor binding in the DmpF protomer may be correlated with channeling and activity at the DmpG protomer. In the presence of NAD+ a 29-A-long sequestered tunnel links the two active sites. Two barriers are visible along the tunnel and suggest control points for the movement of the reactive and volatile acetaldehyde intermediate between the two active sites.


    Organizational Affiliation

    Department of Molecular, Cellular and Developmental Biology Sinsheimer Laboratory, 1156 High Street, University of California, Santa Cruz, CA 95064, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
4-hydroxy-2-oxovalerate aldolase
A, C, E, G
345Pseudomonas sp. (strain CF600)Gene Names: dmpG
EC: 4.1.3.39
Find proteins for P51016 (Pseudomonas sp. (strain CF600))
Go to UniProtKB:  P51016
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
acetaldehyde dehydrogenase (acylating)
B, D, F, H
312Pseudomonas sp. (strain CF600)Gene Names: dmpF
EC: 1.2.1.10
Find proteins for Q52060 (Pseudomonas sp. (strain CF600))
Go to UniProtKB:  Q52060
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, C, E, G
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, C, E, F, G
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NAD
Query on NAD

Download SDF File 
Download CCD File 
B, D, H
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
OXL
Query on OXL

Download SDF File 
Download CCD File 
A, C, E, G
OXALATE ION
C2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-L
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A, B, C, E, G
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 102.200α = 90.00
b = 140.000β = 90.00
c = 191.400γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
SnBphasing
REFMACrefinement
DENZOdata reduction
HKL-2000data collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-17
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Advisory, Refinement description