4H2H

Crystal structure of an enolase (mandalate racemase subgroup, target EFI-502101) from Pelagibaca bermudensis htcc2601, with bound mg and l-4-hydroxyproline betaine (betonicine)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery of new enzymes and metabolic pathways by using structure and genome context.

Zhao, S.Kumar, R.Sakai, A.Vetting, M.W.Wood, B.M.Brown, S.Bonanno, J.B.Hillerich, B.S.Seidel, R.D.Babbitt, P.C.Almo, S.C.Sweedler, J.V.Gerlt, J.A.Cronan, J.E.Jacobson, M.P.

(2013) Nature 502: 698-702

  • DOI: 10.1038/nature12576
  • Primary Citation of Related Structures:  2PMQ

  • PubMed Abstract: 
  • Assigning valid functions to proteins identified in genome projects is challenging: overprediction and database annotation errors are the principal concerns. We and others are developing computation-guided strategies for functional discovery with 'me ...

    Assigning valid functions to proteins identified in genome projects is challenging: overprediction and database annotation errors are the principal concerns. We and others are developing computation-guided strategies for functional discovery with 'metabolite docking' to experimentally derived or homology-based three-dimensional structures. Bacterial metabolic pathways often are encoded by 'genome neighbourhoods' (gene clusters and/or operons), which can provide important clues for functional assignment. We recently demonstrated the synergy of docking and pathway context by 'predicting' the intermediates in the glycolytic pathway in Escherichia coli. Metabolite docking to multiple binding proteins and enzymes in the same pathway increases the reliability of in silico predictions of substrate specificities because the pathway intermediates are structurally similar. Here we report that structure-guided approaches for predicting the substrate specificities of several enzymes encoded by a bacterial gene cluster allowed the correct prediction of the in vitro activity of a structurally characterized enzyme of unknown function (PDB 2PMQ), 2-epimerization of trans-4-hydroxy-L-proline betaine (tHyp-B) and cis-4-hydroxy-D-proline betaine (cHyp-B), and also the correct identification of the catabolic pathway in which Hyp-B 2-epimerase participates. The substrate-liganded pose predicted by virtual library screening (docking) was confirmed experimentally. The enzymatic activities in the predicted pathway were confirmed by in vitro assays and genetic analyses; the intermediates were identified by metabolomics; and repression of the genes encoding the pathway by high salt concentrations was established by transcriptomics, confirming the osmolyte role of tHyp-B. This study establishes the utility of structure-guided functional predictions to enable the discovery of new metabolic pathways.


    Organizational Affiliation

    1] Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA [2].




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mandelate racemase/muconate lactonizing enzyme
A, B, C, D, E, F, G, H
376Pelagibaca bermudensis (strain JCM 13377 / KCTC 12554 / HTCC2601)Gene Names: hpbD
EC: 5.1.1.-
Find proteins for Q0FPQ4 (Pelagibaca bermudensis (strain JCM 13377 / KCTC 12554 / HTCC2601))
Go to UniProtKB:  Q0FPQ4
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0XW
Query on 0XW

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A, B, C, D, E, F, G, H
(2S,4R)-4-hydroxy-1,1-dimethylpyrrolidinium-2-carboxylate
Betonicine, L-4-Hydroxyproline betaine
C7 H13 N O3
MUNWAHDYFVYIKH-RITPCOANSA-N
 Ligand Interaction
IOD
Query on IOD

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Download CCD File 
A, B, C, D, E, F, G, H
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B, C, D, E, F, G, H
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

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A, B
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

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Download CCD File 
C, D, E
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.159 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 91.035α = 90.00
b = 152.824β = 105.20
c = 113.027γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-10
    Type: Initial release
  • Version 1.1: 2013-09-18
    Type: Database references
  • Version 1.2: 2013-11-06
    Type: Database references