4J1O

Crystal structure of an enolase (mandelate racemase subgroup) from paracococus denitrificans pd1222 (target nysgrc-012907) with bound l-proline betaine (substrate)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine.

Kumar, R.Zhao, S.Vetting, M.W.Wood, B.M.Sakai, A.Cho, K.Solbiati, J.Almo, S.C.Sweedler, J.V.Jacobson, M.P.Gerlt, J.A.Cronan, J.E.

(2014) mBio 5: e00933-e00913

  • DOI: 10.1128/mBio.00933-13
  • Primary Citation of Related Structures:  
    4E8G, 4IZG, 4J1O

  • PubMed Abstract: 
  • Through the use of genetic, enzymatic, metabolomic, and structural analyses, we have discovered the catabolic pathway for proline betaine, an osmoprotectant, in Paracoccus denitrificans and Rhodobacter sphaeroides. Genetic and enzymatic analyses showed that several of the key enzymes of the hydroxyproline betaine degradation pathway also function in proline betaine degradation ...

    Through the use of genetic, enzymatic, metabolomic, and structural analyses, we have discovered the catabolic pathway for proline betaine, an osmoprotectant, in Paracoccus denitrificans and Rhodobacter sphaeroides. Genetic and enzymatic analyses showed that several of the key enzymes of the hydroxyproline betaine degradation pathway also function in proline betaine degradation. Metabolomic analyses detected each of the metabolic intermediates of the pathway. The proline betaine catabolic pathway was repressed by osmotic stress and cold stress, and a regulatory transcription factor was identified. We also report crystal structure complexes of the P. denitrificans HpbD hydroxyproline betaine epimerase/proline betaine racemase with l-proline betaine and cis-hydroxyproline betaine.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mandelate racemase/muconate lactonizing enzyme, N-terminal domain proteinA, B391Paracoccus denitrificans PD1222Mutation(s): 0 
Gene Names: hpbDPden_1187
EC: 5.1.1.22
UniProt
Find proteins for A1B198 (Paracoccus denitrificans (strain Pd 1222))
Explore A1B198 
Go to UniProtKB:  A1B198
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1B198
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PBE
Query on PBE

Download Ideal Coordinates CCD File 
N [auth A],
U [auth B]
1,1-DIMETHYL-PROLINIUM
C7 H14 N O2
CMUNUTVVOOHQPW-LURJTMIESA-O
 Ligand Interaction
IOD
Query on IOD

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
Q [auth B],
R [auth B],
S [auth B],
T [auth B]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
M [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
O [auth B],
P [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.297α = 90
b = 117.297β = 90
c = 110.528γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-06
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Database references