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: 1.6 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.158 

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:  

  • 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 show ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein
A, B
391Paracoccus denitrificans (strain Pd 1222)Mutation(s): 0 
Gene Names: hpbD
EC: 5.1.1.22
Find proteins for A1B198 (Paracoccus denitrificans (strain Pd 1222))
Go to UniProtKB:  A1B198
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

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A, B
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
PBE
Query on PBE

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Download CCD File 
A, B
1,1-DIMETHYL-PROLINIUM
PROLINE BETAINE
C7 H14 N O2
CMUNUTVVOOHQPW-LURJTMIESA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.158 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 117.297α = 90.00
b = 117.297β = 90.00
c = 110.528γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHENIXphasing
SCALAdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

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