4DR9

Crystal structure of a peptide deformylase from synechococcus elongatus in complex with actinonin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Structure and function of a cyanophage-encoded peptide deformylase.

Frank, J.A.Lorimer, D.Youle, M.Witte, P.Craig, T.Abendroth, J.Rohwer, F.Edwards, R.A.Segall, A.M.Burgin, A.B.

(2013) ISME J 7: 1150-1160

  • DOI: 10.1038/ismej.2013.4
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bacteriophages encode auxiliary metabolic genes that support more efficient phage replication. For example, cyanophages carry several genes to maintain host photosynthesis throughout infection, shuttling the energy and reducing power generated away f ...

    Bacteriophages encode auxiliary metabolic genes that support more efficient phage replication. For example, cyanophages carry several genes to maintain host photosynthesis throughout infection, shuttling the energy and reducing power generated away from carbon fixation and into anabolic pathways. Photodamage to the D1/D2 proteins at the core of photosystem II necessitates their continual replacement. Synthesis of functional proteins in bacteria requires co-translational removal of the N-terminal formyl group by a peptide deformylase (PDF). Analysis of marine metagenomes to identify phage-encoded homologs of known metabolic genes found that marine phages carry PDF genes, suggesting that their expression during infection might benefit phage replication. We identified a PDF homolog in the genome of Synechococcus cyanophage S-SSM7. Sequence analysis confirmed that it possesses the three absolutely conserved motifs that form the active site in PDF metalloproteases. Phylogenetic analysis placed it within the Type 1B subclass, most closely related to the Arabidopsis chloroplast PDF, but lacking the C-terminal α-helix characteristic of that group. PDF proteins from this phage and from Synechococcus elongatus were expressed and characterized. The phage PDF is the more active enzyme and deformylates the N-terminal tetrapeptides from D1 proteins more efficiently than those from ribosomal proteins. Solution of the X-ray/crystal structures of those two PDFs to 1.95 Å resolution revealed active sites identical to that of the Type 1B Arabidopsis chloroplast PDF. Taken together, these findings show that many cyanophages encode a PDF with a D1 substrate preference that adds to the repertoire of genes used by phages to maintain photosynthetic activities.


    Organizational Affiliation

    Department of Biology, San Diego State University, San Diego, CA 92182-7720, USA. jeralfrank@gmail.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptide deformylase
A, B, C, D
192Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1)Gene Names: def
EC: 3.5.1.88
Find proteins for A0A0H3JZJ4 (Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1))
Go to UniProtKB:  A0A0H3JZJ4
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
BR
Query on BR

Download SDF File 
Download CCD File 
A, B, C, D
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
BB2
Query on BB2

Download SDF File 
Download CCD File 
A, B, C, D
ACTINONIN
2-[(FORMYL-HYDROXY-AMINO)-METHYL]-HEPTANOIC ACID [1-(2-HYDROXYMETHYL-PYRROLIDINE-1-CARBONYL)-2-METHYL-PROPYL]-AMIDE
C19 H35 N3 O5
XJLATMLVMSFZBN-VYDXJSESSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BB2IC50: 10 nM BINDINGMOAD
BB2IC50: 10 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.182 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 43.250α = 80.87
b = 65.780β = 76.82
c = 68.290γ = 82.75
Software Package:
Software NamePurpose
REFMACrefinement
JDirectordata collection
XSCALEdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-16
    Type: Initial release
  • Version 1.1: 2013-03-06
    Type: Database references
  • Version 1.2: 2013-06-05
    Type: Database references
  • Version 1.3: 2013-07-10
    Type: Database references
  • Version 1.4: 2017-11-15
    Type: Refinement description
  • Version 1.5: 2018-04-11
    Type: Data collection