1NVM

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 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 U S A 100: 6992-6997

  • DOI: 10.1073/pnas.1236794100
  • Primary Citation of Related Structures:  
    1NVM

  • 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 anomalous dispersion (MAD) techniques and refined to 1 ...

    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.


    Related Citations: 
    • Crystallization and preliminary X-ray analysis of dmpFG-encoded 4-hydroxy-2-ketovalerate aldolase-aldehyde dehydrogenase (acylating) from Pseudomonas sp.strain CF600
      (2001) Acta Crystallogr D Biol Crystallogr 57: 582

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
4-hydroxy-2-oxovalerate aldolaseA, C, E, G345Pseudomonas sp. CF600Mutation(s): 0 
Gene Names: dmpG
EC: 4.1.3 (PDB Primary Data), 4.1.3.39 (UniProt)
Find proteins for P51016 (Pseudomonas sp. (strain CF600))
Explore P51016 
Go to UniProtKB:  P51016
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
acetaldehyde dehydrogenase (acylating)B, D, F, H312Pseudomonas sp. CF600Mutation(s): 0 
Gene Names: dmpF
EC: 1.2.1.10
Find proteins for Q52060 (Pseudomonas sp. (strain CF600))
Explore Q52060 
Go to UniProtKB:  Q52060
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
KA [auth H], N [auth B], W [auth D]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
MPD
Query on MPD

Download Ideal Coordinates CCD File 
CA [auth E], JA [auth G], M [auth A], O [auth B], U [auth C], V [auth C](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth E] , BA [auth E] , DA [auth F] , EA [auth F] , HA [auth G] , IA [auth G] , K [auth A] , L [auth A] , 
AA [auth E],  BA [auth E],  DA [auth F],  EA [auth F],  HA [auth G],  IA [auth G],  K [auth A],  L [auth A],  R [auth C],  S [auth C],  T [auth C],  Z [auth E]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
OXL
Query on OXL

Download Ideal Coordinates CCD File 
GA [auth G], J [auth A], Q [auth C], Y [auth E]OXALATE ION
C2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-L
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
FA [auth G], I [auth A], P [auth C], X [auth E]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.2α = 90
b = 140β = 90
c = 191.4γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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