5A02

Crystal structure of aldose-aldose oxidoreductase from Caulobacter crescentus complexed with glycerol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 

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This is version 1.2 of the entry. See complete history


Literature

Structure and Function of Caulobacter Crescentus Aldose-Aldose Oxidoreductase.

Taberman, H.Andberg, M.Koivula, A.Hakulinen, N.Penttila, M.Rouvinen, J.Parkkinen, T.

(2015) Biochem J 472: 297

  • DOI: 10.1042/BJ20150681
  • Primary Citation of Related Structures:  
    5A02, 5A03, 5A04, 5A05, 5A06

  • PubMed Abstract: 
  • Aldose-aldose oxidoreductase (Cc AAOR) is a recently characterized enzyme from the bacterial strain Caulobacter crescentus CB15 belonging to the glucose-fructose oxidoreductase/inositol dehydrogenase/rhizopine catabolism protein (Gfo/Idh/MocA) family. Cc AAOR catalyses the oxidation and reduction of a panel of aldose monosaccharides using a tightly bound NADP(H) cofactor that is regenerated in the catalytic cycle ...

    Aldose-aldose oxidoreductase (Cc AAOR) is a recently characterized enzyme from the bacterial strain Caulobacter crescentus CB15 belonging to the glucose-fructose oxidoreductase/inositol dehydrogenase/rhizopine catabolism protein (Gfo/Idh/MocA) family. Cc AAOR catalyses the oxidation and reduction of a panel of aldose monosaccharides using a tightly bound NADP(H) cofactor that is regenerated in the catalytic cycle. Furthermore, Cc AAOR can also oxidize 1,4-linked oligosaccharides. In the present study, we present novel crystal structures of the dimeric Cc AAOR in complex with the cofactor and glycerol, D-xylose, D-glucose, maltotriose and D-sorbitol determined to resolutions of 2.0, 1.8, 1.7, 1.9 and 1.8 Å (1 Å=0.1 nm), respectively. These complex structures allowed for a detailed analysis of the ligand-binding interactions. The structures showed that the C1 carbon of a substrate, which is either reduced or oxidized, is close to the reactive C4 carbon of the nicotinamide ring of NADP(H). In addition, the O1 hydroxy group of the substrate, which is either protonated or deprotonated, is unexpectedly close to both Lys(104) and Tyr(189), which may both act as a proton donor or acceptor. This led us to hypothesize that this intriguing feature could be beneficial for Cc AAOR to catalyse the reduction of a linear form of a monosaccharide substrate and the oxidation of a pyranose form of the same substrate in a reaction cycle, during which the bound cofactor is regenerated.


    Organizational Affiliation

    Department of Chemistry, University of Eastern Finland, PO Box 111, FI-80101 Joensuu, Finland tarja.parkkinen@uef.fi.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ALDOSE-ALDOSE OXIDOREDUCTASE
A, B, C, D, E, F
A, B, C, D, E, F
339Caulobacter vibrioides CB15Mutation(s): 0 
Gene Names: CC_1225
EC: 1.1.99
UniProt
Find proteins for Q9A8X3 (Caulobacter vibrioides (strain ATCC 19089 / CB15))
Explore Q9A8X3 
Go to UniProtKB:  Q9A8X3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9A8X3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download Ideal Coordinates CCD File 
FA [auth F],
G [auth A],
K [auth B],
N [auth C],
S [auth D],
FA [auth F],
G [auth A],
K [auth B],
N [auth C],
S [auth D],
Y [auth E]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
DA [auth E],
EA [auth E],
J [auth A],
P [auth C],
Q [auth C],
DA [auth E],
EA [auth E],
J [auth A],
P [auth C],
Q [auth C],
R [auth C],
W [auth D],
X [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth E],
BA [auth E],
CA [auth E],
GA [auth F],
H [auth A],
AA [auth E],
BA [auth E],
CA [auth E],
GA [auth F],
H [auth A],
HA [auth F],
I [auth A],
IA [auth F],
JA [auth F],
L [auth B],
M [auth B],
O [auth C],
T [auth D],
U [auth D],
V [auth D],
Z [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.31α = 90
b = 153.59β = 109.85
c = 108.01γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-21
    Type: Initial release
  • Version 1.1: 2015-11-25
    Changes: Source and taxonomy
  • Version 1.2: 2015-12-09
    Changes: Database references