4J0Q

Crystal structure of Pseudomonas putida elongation factor Tu (EF-Tu)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.294 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Human oxygen sensing may have origins in prokaryotic elongation factor Tu prolyl-hydroxylation

Scotti, J.S.Leung, I.K.H.Ge, W.Bentley, M.A.Paps, J.Kramer, H.B.Lee, J.Aik, W.Choi, H.Paulsen, S.M.Bowman, L.A.H.Loik, N.D.Horita, S.Ho, C.H.Kershaw, N.J.Tang, C.M.Claridge, T.D.W.Preston, G.M.McDonough, M.A.Schofield, C.J.

(2014) Proc.Natl.Acad.Sci.USA 111: 13331-13336

  • DOI: 10.1073/pnas.1409916111
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The roles of 2-oxoglutarate (2OG)-dependent prolyl-hydroxylases in eukaryotes include collagen stabilization, hypoxia sensing, and translational regulation. The hypoxia-inducible factor (HIF) sensing system is conserved in animals, but not in other o ...

    The roles of 2-oxoglutarate (2OG)-dependent prolyl-hydroxylases in eukaryotes include collagen stabilization, hypoxia sensing, and translational regulation. The hypoxia-inducible factor (HIF) sensing system is conserved in animals, but not in other organisms. However, bioinformatics imply that 2OG-dependent prolyl-hydroxylases (PHDs) homologous to those acting as sensing components for the HIF system in animals occur in prokaryotes. We report cellular, biochemical, and crystallographic analyses revealing that Pseudomonas prolyl-hydroxylase domain containing protein (PPHD) contain a 2OG oxygenase related in structure and function to the animal PHDs. A Pseudomonas aeruginosa PPHD knockout mutant displays impaired growth in the presence of iron chelators and increased production of the virulence factor pyocyanin. We identify elongation factor Tu (EF-Tu) as a PPHD substrate, which undergoes prolyl-4-hydroxylation on its switch I loop. A crystal structure of PPHD reveals striking similarity to human PHD2 and a Chlamydomonas reinhardtii prolyl-4-hydroxylase. A crystal structure of PPHD complexed with intact EF-Tu reveals that major conformational changes occur in both PPHD and EF-Tu, including a >20-Å movement of the EF-Tu switch I loop. Comparison of the PPHD structures with those of HIF and collagen PHDs reveals conservation in substrate recognition despite diverse biological roles and origins. The observed changes will be useful in designing new types of 2OG oxygenase inhibitors based on various conformational states, rather than active site iron chelators, which make up most reported 2OG oxygenase inhibitors. Structurally informed phylogenetic analyses suggest that the role of prolyl-hydroxylation in human hypoxia sensing has ancient origins.


    Organizational Affiliation

    Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Elongation factor Tu-A
A, B, C, D, E
433Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440)Mutation(s): 0 
Gene Names: tufA (tuf-1)
Find proteins for Q88QP8 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440))
Go to UniProtKB:  Q88QP8
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A, B, C, D, E
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A, C, D, E
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
MES
Query on MES

Download SDF File 
Download CCD File 
A, B, E
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.294 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.174 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 212.505α = 90.00
b = 155.624β = 114.76
c = 99.298γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
DENZOdata reduction
GDAdata collection
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-05
    Type: Initial release
  • Version 1.1: 2014-09-17
    Type: Database references
  • Version 1.2: 2014-10-01
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Refinement description