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PDBsum entry 1xem

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protein ligands metals links
Hydrolase PDB id
1xem
Jmol
Contents
Protein chain
164 a.a. *
Ligands
FMT ×10
Metals
_ZN
Waters ×304
* Residue conservation analysis
PDB id:
1xem
Name: Hydrolase
Title: High resolution crystal structure of escherichia coli zinc- deformylase bound to formate
Structure: Peptide deformylase. Chain: a. Synonym: pdf, polypeptide deformylase. Ec: 3.5.1.88
Source: Escherichia coli. Organism_taxid: 469008. Strain: bl21(de3)
Resolution:
1.76Å     R-factor:   0.163     R-free:   0.204
Authors: R.Jain,B.Hao,R.-P.Liu,M.K.Chan
Key ref: R.Jain et al. (2005). Structures of E. coli peptide deformylase bound to formate: insight into the preference for Fe2+ over Zn2+ as the active site metal. J Am Chem Soc, 127, 4558-4559. PubMed id: 15796505 DOI: 10.1021/ja0503074
Date:
10-Sep-04     Release date:   29-Mar-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0A6K3  (DEF_ECOLI) -  Peptide deformylase
Seq:
Struc:
169 a.a.
164 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.5.1.88  - Peptide deformylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Formyl-L-methionyl peptide + H2O = formate + methionyl peptide
Formyl-L-methionyl peptide
+ H(2)O
=
formate
Bound ligand (Het Group name = FMT)
corresponds exactly
+ methionyl peptide
      Cofactor: Fe(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     translation   3 terms 
  Biochemical function     protein binding     8 terms  

 

 
    reference    
 
 
DOI no: 10.1021/ja0503074 J Am Chem Soc 127:4558-4559 (2005)
PubMed id: 15796505  
 
 
Structures of E. coli peptide deformylase bound to formate: insight into the preference for Fe2+ over Zn2+ as the active site metal.
R.Jain, B.Hao, R.P.Liu, M.K.Chan.
 
  ABSTRACT  
 
E. coli peptide deformylase (PDF) catalyzes the deformylation of nascent polypeptides generated during protein synthesis. While PDF was originally thought to be a zinc enzyme, subsequent studies revealed that the active site metal is iron. In an attempt to understand this unusual metal preference, high-resolution structures of Fe-, Co-, and Zn-PDF were determined in complex with its deformylation product, formate. In all three structures, the formate ion binds the metal and forms hydrogen-bonding interactions with the backbone nitrogen of Leu91, the amide side chain of Gln50, and the carboxylate side chain of Glu133. One key difference, however, is how the formate binds the metal. In Fe-PDF and Co-PDF, formate binds in a bidentate fashion, while in Zn-PDF, it binds in a monodentate fashion. Importantly, these structural results provide the first clues into the origins of PDF's metal-dependent activity differences. On the basis of these structures, we propose that the basis for the higher activity of Fe-PDF stems from the better ability of iron to bind and activate the tetrahedral transition state required for cleavage of the N-terminal formyl group.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21338418 J.E.Martin, and J.A.Imlay (2011).
The alternative aerobic ribonucleotide reductase of Escherichia coli, NrdEF, is a manganese-dependent enzyme that enables cell replication during periods of iron starvation.
  Mol Microbiol, 80, 319-334.  
20136146 M.Hernick, S.G.Gattis, J.E.Penner-Hahn, and C.A.Fierke (2010).
Activation of Escherichia coli UDP-3-O-[(R)-3-hydroxymyristoyl]-N-acetylglucosamine deacetylase by Fe2+ yields a more efficient enzyme with altered ligand affinity.
  Biochemistry, 49, 2246-2255.  
18467349 J.Song, H.Tan, K.Takemoto, and T.Akutsu (2008).
HSEpred: predict half-sphere exposure from protein sequences.
  Bioinformatics, 24, 1489-1497.  
17977509 K.T.Nguyen, J.C.Wu, J.A.Boylan, F.C.Gherardini, and D.Pei (2007).
Zinc is the metal cofactor of Borrelia burgdorferi peptide deformylase.
  Arch Biochem Biophys, 468, 217-225.  
16733568 F.Namuswe, and D.P.Goldberg (2006).
A combinatorial approach to minimal peptide models of a metalloprotein active site.
  Chem Commun (Camb), (), 2326-2328.  
16471944 V.V.Karambelkar, C.Xiao, Y.Zhang, A.A.Sarjeant, and D.P.Goldberg (2006).
Geometric preferences in iron(II) and zinc(II) model complexes of peptide deformylase.
  Inorg Chem, 45, 1409-1411.  
16192279 S.Fieulaine, C.Juillan-Binard, A.Serero, F.Dardel, C.Giglione, T.Meinnel, and J.L.Ferrer (2005).
The crystal structure of mitochondrial (Type 1A) peptide deformylase provides clear guidelines for the design of inhibitors specific for the bacterial forms.
  J Biol Chem, 280, 42315-42324.
PDB codes: 1zxz 1zy0 1zy1
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.