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PDBsum entry 1ix1
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* Residue conservation analysis
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PDB id:
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Hydrolase
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Title:
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Crystal structure of p.Aeruginosa peptide deformylase complexed with antibiotic actinonin
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Structure:
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Peptide deformylase. Chain: a, b. Synonym: pdf, polypeptide deformylase. Engineered: yes
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Source:
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Pseudomonas aeruginosa. Organism_taxid: 287. Expressed in: escherichia coli. Expression_system_taxid: 562.
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Resolution:
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1.85Å
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R-factor:
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0.185
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R-free:
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0.214
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Authors:
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H.-W.Kim,H.-J.Yoon,J.Y.Lee,B.W.Han,J.K.Yang,B.I.Lee,H.J.Ahn,H.H.Lee, S.W.Suh
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Key ref:
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H.J.Yoon
et al.
(2004).
Crystal structure of peptide deformylase from Staphylococcus aureus in complex with actinonin, a naturally occurring antibacterial agent.
Proteins,
57,
639-642.
PubMed id:
DOI:
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Date:
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07-Jun-02
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Release date:
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09-Sep-03
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PROCHECK
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Headers
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References
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Q9I7A8
(DEF_PSEAE) -
Peptide deformylase from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
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Seq:
Struc:
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168 a.a.
169 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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Enzyme class:
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E.C.3.5.1.88
- peptide deformylase.
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Reaction:
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N-terminal N-formyl-L-methionyl-[peptide] + H2O = N-terminal L-methionyl- [peptide] + formate
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N-terminal N-formyl-L-methionyl-[peptide]
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+
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H2O
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=
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N-terminal L-methionyl- [peptide]
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+
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formate
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Cofactor:
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Fe(2+)
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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DOI no:
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Proteins
57:639-642
(2004)
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PubMed id:
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Crystal structure of peptide deformylase from Staphylococcus aureus in complex with actinonin, a naturally occurring antibacterial agent.
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H.J.Yoon,
H.L.Kim,
S.K.Lee,
H.W.Kim,
H.W.Kim,
J.Y.Lee,
B.Mikami,
S.W.Suh.
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ABSTRACT
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Selected figure(s)
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Figure 1.
Figure 1. (a) Amino acid sequence alignment of seven peptide
deformylases. Strictly conserved residues and semi-conserved
residues are colored pink and yellow. Blue boxes represent three
conserved motifs. The residue numbers are for SaPDF. SA is for
peptide deformylase from S. aureus (PDB codes 1Q1Y, 1LM4), PA
for P. aeruginosa (1IX1, 1LRY, 1N5N), EC for E. coli (1BSZ), TM
for T. martima (1LME), PF for P. falciparum (1JYM), BS for B.
stearothermophilus (1LQY) and SP for S. pneumoniae (1LM6). (b)
Stereo view of the superimposed C  backbones
of SaPDF (blue) and PaPDF (orange). The spheres indicate Zn^2+
ions (SaPDF, cyan; PaPDF, magenta). (c) Stereo view of the
superposition of the active sites of SaPDF and PaPDF with bound
actinonin. C backbones
of SaPDF and PaPDF are shown in blue and orange lines,
respectively. The inhibitor actinonin (SaPDF, cyan; PaPDF,
magenta) and the Zn^2+ ion (SaPDF, cyan; PaPDF, magenta) are
drawn in ball-and-stick representation.
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The above figure is
reprinted
by permission from John Wiley & Sons, Inc.:
Proteins
(2004,
57,
639-642)
copyright 2004.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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S.Escobar-Alvarez,
Y.Goldgur,
G.Yang,
O.Ouerfelli,
Y.Li,
and
D.A.Scheinberg
(2009).
Structure and activity of human mitochondrial peptide deformylase, a novel cancer target.
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J Mol Biol,
387,
1211-1228.
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PDB codes:
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B.M.McArdle,
and
R.J.Quinn
(2007).
Identification of protein fold topology shared between different folds inhibited by natural products.
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Chembiochem,
8,
788-798.
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K.Ohlsen,
and
U.Lorenz
(2007).
Novel targets for antibiotics in Staphylococcus aureus.
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Future Microbiol,
2,
655-666.
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J.Cai,
C.Han,
T.Hu,
J.Zhang,
D.Wu,
F.Wang,
Y.Liu,
J.Ding,
K.Chen,
J.Yue,
X.Shen,
and
H.Jiang
(2006).
Peptide deformylase is a potential target for anti-Helicobacter pylori drugs: reverse docking, enzymatic assay, and X-ray crystallography validation.
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Protein Sci,
15,
2071-2081.
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PDB codes:
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
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Links
