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 

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This is version 1.4 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: https://doi.org/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 1.7-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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4-hydroxy-2-oxovalerate aldolase
A, C, E, G
345Pseudomonas sp. CF600Mutation(s): 0 
Gene Names: DMPG
EC: 4.1.3
UniProt
Find proteins for P51016 (Pseudomonas sp. (strain CF600))
Explore P51016 
Go to UniProtKB:  P51016
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51016
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
acetaldehyde dehydrogenase (acylating)
B, D, F, H
312Pseudomonas sp. CF600Mutation(s): 0 
Gene Names: DMPF
EC: 1.2.1.10
UniProt
Find proteins for Q52060 (Pseudomonas sp. (strain CF600))
Explore Q52060 
Go to UniProtKB:  Q52060
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ52060
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / 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
MPD
Query on MPD

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CA [auth E]
JA [auth G]
M [auth A]
O [auth B]
U [auth C]
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
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth E]
DA [auth F]
EA [auth F]
HA [auth G]
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
OXL
Query on OXL

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GA [auth G],
J [auth A],
Q [auth C],
Y [auth E]
OXALATE ION
C2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-L
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
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

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Ligand Structure Quality Assessment 


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
  • Version 1.4: 2024-02-14
    Changes: Advisory, Data collection, Database references, Derived calculations