DB code: S00442

RLCP classification 1.13.11100.561 : Hydrolysis
CATH domain 3.90.45.10 : Peptide Deformylase Catalytic domain
E.C. 3.5.1.88
CSA 1bs4 1bsj
M-CSA 1bs4 1bsj
MACiE M0098

CATH domain Related DB codes (homologues)

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P0A6K3 Peptide deformylase
PDF
EC 3.5.1.88
Polypeptide deformylase
NP_417745.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_492146.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF01327 (Pep_deformylase)
[Graphical View]

KEGG enzyme name
peptide deformylase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P0A6K3 DEF_ECOLI Formyl-L-methionyl peptide + H(2)O = formate + methionyl peptide. Monomer. Binds 1 Fe(2+) ion per monomer.

KEGG Pathways
Map code Pathways E.C.

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00023 C11439 C00001 C00058 C11440
E.C.
Compound Fe2+ Formyl-L-methionyl peptide H2O Formate Methionyl peptide
Type heavy metal amide group,peptide/protein,sulfide group H2O carboxyl group peptide/protein,sulfide group
ChEBI 18248
 82664
 18248
 82664
 		15377
 15377
 		30751
 30751
PubChem 23925
 23925
 		22247451
 962
 22247451
 962
 		18971002
 284
 18971002
 284
1bs4A Analogue:_ZN Unbound Unbound Unbound Unbound
1bs4B Analogue:_ZN Unbound Unbound Unbound Unbound
1bs4C Analogue:_ZN Unbound Unbound Unbound Unbound
1bs5A Analogue:_ZN Unbound Unbound Unbound Unbound
1bs5B Analogue:_ZN Unbound Unbound Unbound Unbound
1bs5C Analogue:_ZN Unbound Unbound Unbound Unbound
1bs6A Analogue:_NI Unbound Unbound Bound:MET-ALA-SER Unbound
1bs6B Analogue:_NI Unbound Unbound Bound:MET-ALA-SER Unbound
1bs6C Analogue:_NI Unbound Unbound Bound:MET-ALA-SER Unbound
1bs7A Analogue:_NI Unbound Unbound Unbound Unbound
1bs7B Analogue:_NI Unbound Unbound Unbound Unbound
1bs7C Analogue:_NI Unbound Unbound Unbound Unbound
1bs8A Analogue:_ZN Unbound Unbound Bound:MET-ALA-SER Unbound
1bs8B Analogue:_ZN Unbound Unbound Bound:MET-ALA-SER Unbound
1bs8C Analogue:_ZN Unbound Unbound Bound:MET-ALA-SER Unbound
1bsjA Analogue:_CO Unbound Unbound Unbound Transition-state-analogue:MLN
1bskA Analogue:_ZN Unbound Unbound Unbound Transition-state-analogue:MLN
1bszA Bound:_FE Unbound Unbound Unbound Unbound
1bszB Bound:_FE Unbound Unbound Unbound Unbound
1bszC Bound:_FE Unbound Unbound Unbound Unbound
1defA Analogue:_ZN Unbound Unbound Unbound Unbound
1dffA Analogue:_ZN Unbound Unbound Unbound Unbound
1icjA Analogue:_NI Unbound Unbound Unbound Unbound
1icjB Analogue:_NI Unbound Unbound Unbound Unbound
1icjC Analogue:_NI Unbound Unbound Unbound Unbound
2defA Analogue:_NI Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1bs4A GLN 50;GLU 133 CYS 90;HIS 132;HIS 136(Fe binding) LEU 91
1bs4B GLN 550;GLU 633 CYS 590;HIS 632;HIS 636(Fe binding) LEU 591
1bs4C GLN 1050;GLU 1133 CYS 1090;HIS 1132;HIS 1136(Fe binding) LEU 1091
1bs5A GLN 50;GLU 133 CYS 90;HIS 132;HIS 136(Fe binding) LEU 91
1bs5B GLN 550;GLU 633 CYS 590;HIS 632;HIS 636(Fe binding) LEU 591
1bs5C GLN 1050;GLU 1133 CYS 1090;HIS 1132;HIS 1136(Fe binding) LEU 1091
1bs6A GLN 50;GLU 133 CYS 90;HIS 132;HIS 136(Fe binding) LEU 91
1bs6B GLN 550;GLU 633 CYS 590;HIS 632;HIS 636(Fe binding) LEU 591
1bs6C GLN 1050;GLU 1133 CYS 1090;HIS 1132;HIS 1136(Fe binding) LEU 1091
1bs7A GLN 50;GLU 133 CYS 90;HIS 132;HIS 136(Fe binding) LEU 91
1bs7B GLN 550;GLU 633 CYS 590;HIS 632;HIS 636(Fe binding) LEU 591
1bs7C GLN 1050;GLU 1133 CYS 1090;HIS 1132;HIS 1136(Fe binding) LEU 1091
1bs8A GLN 50;GLU 133 CYS 90;HIS 132;HIS 136(Fe binding) LEU 91
1bs8B GLN 550;GLU 633 CYS 590;HIS 632;HIS 636(Fe binding) LEU 591
1bs8C GLN 1050;GLU 1133 CYS 1090;HIS 1132;HIS 1136(Fe binding) LEU 1091
1bsjA GLN 50;GLU 133 CYS 90;HIS 132;HIS 136(Fe binding) LEU 91
1bskA GLN 50;GLU 133 CYS 90;HIS 132;HIS 136(Fe binding) LEU 91
1bszA GLN 50;GLU 133 CYS 90;HIS 132;HIS 136(Fe binding) LEU 91
1bszB GLN 550;GLU 633 CYS 590;HIS 632;HIS 636(Fe binding) LEU 591
1bszC GLN 1050;GLU 1133 CYS 1090;HIS 1132;HIS 1136(Fe binding) LEU 1091
1defA GLN 50;GLU 133 CYS 90;HIS 132;HIS 136(Fe binding) LEU 91
1dffA GLN 50;GLU 133 CYS 90;HIS 132;HIS 136(Fe binding) LEU 91
1icjA GLN 50;GLU 133 CYS 90;HIS 132;HIS 136(Fe binding) LEU 91
1icjB GLN 550;GLU 633 CYS 590;HIS 632;HIS 636(Fe binding) LEU 591
1icjC GLN 1050;GLU 1133 CYS 1090;HIS 1132;HIS 1136(Fe binding) LEU 1091
2defA GLN 50;GLU 133 CYS 90;HIS 132;HIS 136(Fe binding) LEU 91

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
p.180-181
[4]
Fig.5, p.13908 2
[5]
p.345-346
[6]
p.11415-11416, Fig.5
[7]
p.507-510
[10]
Fig.3, p.1055-1056 2
[12]
Fig.2, p.1454-1455
[13]
Fig.6, p.4717-4718 2
[14]
Fig.6, p.789-790 2
[23]
p.10567-10569

References
[1]
Resource
Comments
Medline ID
PubMed ID 7490741
Journal J Mol Biol
Year 1995
Volume 254
Pages 175-83
Authors Meinnel T, Lazennec C, Blanquet S
Title Mapping of the active site zinc ligands of peptide deformylase.
Related PDB
Related UniProtKB
[2]
Resource
Comments NMR (solution structure of an active core domain)
Medline ID 97002011
PubMed ID 8845003
Journal J Mol Biol
Year 1996
Volume 262
Pages 375-86
Authors Meinnel T, Blanquet S, Dardel F
Title A new subclass of the zinc metalloproteases superfamily revealed by the solution structure of peptide deformylase.
Related PDB 1def
Related UniProtKB P0A6K3
[3]
Resource
Comments
Medline ID
PubMed ID 9126850
Journal J Mol Biol
Year 1997
Volume 267
Pages 749-61
Authors Meinnel T, Lazennec C, Villoing S, Blanquet S
Title Structure-function relationships within the peptide deformylase family. Evidence for a conserved architecture of the active site involving three conserved motifs and a metal ion.
Related PDB
Related UniProtKB
[4]
Resource
Comments X-ray crystallography (2.9 Angstroms)
Medline ID 98042282
PubMed ID 9374869
Journal Biochemistry
Year 1997
Volume 36
Pages 13904-9
Authors Chan MK, Gong W, Rajagopalan PT, Hao B, Tsai CM, Pei D
Title Crystal structure of the Escherichia coli peptide deformylase.
Related PDB 1dff
Related UniProtKB P0A6K3
[5]
Resource
Comments cofactor
Medline ID 98273280
PubMed ID 9610360
Journal Biochem Biophys Res Commun
Year 1998
Volume 246
Pages 342-6
Authors Groche D, Becker A, Schlichting I, Kabsch W, Schultz S, Wagner AF
Title Isolation and crystallization of functionally competent Escherichia coli peptide deformylase forms containing either iron or nickel in the active site.
Related PDB
Related UniProtKB P0A6K3
[6]
Resource
Comments X-ray crystallography (1.9-2.5 Angstroms)
Medline ID 98234316
PubMed ID 9565550
Journal J Biol Chem
Year 1998
Volume 273
Pages 11413-6
Authors Becker A, Schlichting I, Kabsch W, Schultz S, Wagner AF
Title Structure of peptide deformylase and identification of the substrate binding site.
Related PDB 1bs7 1icj
Related UniProtKB P0A6K3
[7]
Resource
Comments structure by NMR
Medline ID 98332750
PubMed ID 9665852
Journal J Mol Biol
Year 1998
Volume 280
Pages 501-13
Authors Dardel F, Ragusa S, Lazennec C, Blanquet S, Meinnel T
Title Solution structure of nickel-peptide deformylase.
Related PDB
Related UniProtKB P0A6K3
[8]
Resource
Comments
Medline ID
PubMed ID 9665853
Journal J Mol Biol
Year 1998
Volume 280
Pages 515-23
Authors Ragusa S, Blanquet S, Meinnel T
Title Control of peptide deformylase activity by metal cations.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 9712848
Journal J Biol Chem
Year 1998
Volume 273
Pages 22305-10
Authors Rajagopalan PT, Pei D
Title Oxygen-mediated inactivation of peptide deformylase.
Related PDB
Related UniProtKB
[10]
Resource
Comments X-ray crystallography (Fe2+, Ni2+ and Zn2+ forms, complex with the product)
Medline ID 99061332
PubMed ID 9846875
Journal Nat Struct Biol
Year 1998
Volume 5
Pages 1053-8
Authors Becker A, Schlichting I, Kabsch W, Groche D, Schultz S, Wagner AF
Title Iron center, substrate recognition and mechanism of peptide deformylase.
Related PDB 1bs4 1bs5 1bs6 1bs8 1bsz
Related UniProtKB P0A6K3
[11]
Resource
Comments
Medline ID
PubMed ID 9888804
Journal Biochemistry
Year 1999
Volume 38
Pages 643-50
Authors Hu YJ, Wei Y, Zhou Y, Rajagopalan PT, Pei D
Title Determination of substrate specificity for peptide deformylase through the screening of a combinatorial peptide library.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 10373378
Journal J Mol Biol
Year 1999
Volume 289
Pages 1445-57
Authors Ragusa S, Mouchet P, Lazennec C, Dive V, Meinnel T
Title Substrate recognition and selectivity of peptide deformylase. Similarities and differences with metzincins and thermolysin.
Related PDB
Related UniProtKB
[13]
Resource
Comments X-ray crystallography (bound to the transition-state analogue)
Medline ID 99218079
PubMed ID 10200158
Journal Biochemistry
Year 1999
Volume 38
Pages 4712-9
Authors Hao B, Gong W, Rajagopalan PT, Zhou Y, Pei D, Chan MK
Title Structural basis for the design of antibiotics targeting peptide deformylase.
Related PDB 1bsj 1bsk
Related UniProtKB P0A6K3
[14]
Resource
Comments
Medline ID
PubMed ID 10651644
Journal Biochemistry
Year 2000
Volume 39
Pages 779-90
Authors Rajagopalan PT, Grimme S, Pei D
Title Characterization of cobalt(II)-substituted peptide deformylase: function of the metal ion and the catalytic residue Glu-133.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 11429456
Journal Microbiology
Year 2001
Volume 147
Pages 1783-91
Authors Haas M, Beyer D, Gahlmann R, Freiberg C
Title YkrB is the main peptide deformylase in Bacillus subtilis, a eubacterium containing two functional peptide deformylases.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 11733990
Journal J Mol Biol
Year 2001
Volume 314
Pages 695-708
Authors Serero A, Giglione C, Meinnel T
Title Distinctive features of the two classes of eukaryotic peptide deformylases.
Related PDB
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 11747293
Journal Arch Biochem Biophys
Year 2001
Volume 396
Pages 162-70
Authors Bracchi-Ricard V, Nguyen KT, Zhou Y, Rajagopalan PT, Chakrabarti D, Pei D
Title Characterization of an eukaryotic peptide deformylase from Plasmodium falciparum.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 11800612
Journal Inorg Chem
Year 2002
Volume 41
Pages 239-48
Authors Chang S, Karambelkar VV, Sommer RD, Rheingold AL, Goldberg DP
Title New monomeric cobalt(II) and zinc(II) complexes of a mixed N,S(alkylthiolate) ligand: model complexes of (His)(His)(Cys) metalloprotein active sites.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 12005434
Journal Structure (Camb)
Year 2002
Volume 10
Pages 357-67
Authors Kumar A, Nguyen KT, Srivathsan S, Ornstein B, Turley S, Hirsh I, Pei D, Hol WG
Title Crystals of peptide deformylase from Plasmodium falciparum reveal critical characteristics of the active site for drug design.
Related PDB
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 12048187
Journal J Biol Chem
Year 2002
Volume 277
Pages 31163-71
Authors Baldwin ET, Harris MS, Yem AW, Wolfe CL, Vosters AF, Curry KA, Murray RW, Bock JH, Marshall VP, Cialdella JI, Merchant MH, Choi G, Deibel MR Jr
Title Crystal structure of type II peptide deformylase from Staphylococcus aureus.
Related PDB
Related UniProtKB
[21]
Resource
Comments
Medline ID
PubMed ID 12126617
Journal J Mol Biol
Year 2002
Volume 320
Pages 951-62
Authors Guilloteau JP, Mathieu M, Giglione C, Blanc V, Dupuy A, Chevrier M, Gil P, Famechon A, Meinnel T, Mikol V
Title The crystal structures of four peptide deformylases bound to the antibiotic actinonin reveal two distinct types: a platform for the structure-based design of antibacterial agents.
Related PDB
Related UniProtKB
[22]
Resource
Comments
Medline ID
PubMed ID 12127977
Journal Biochem Biophys Res Commun
Year 2002
Volume 295
Pages 884-9
Authors Li Y, Chen Z, Gong W
Title Enzymatic properties of a new peptide deformylase from pathogenic bacterium Leptospira interrogans.
Related PDB
Related UniProtKB
[23]
Resource
Comments
Medline ID
PubMed ID 12173943
Journal Biochemistry
Year 2002
Volume 41
Pages 10563-9
Authors Deng H, Callender R, Zhu J, Nguyen KT, Pei D
Title Determination of the ionization state and catalytic function of Glu-133 in peptide deformylase by difference FTIR spectroscopy.
Related PDB
Related UniProtKB
[24]
Resource
Comments
Medline ID
PubMed ID 12240093
Journal Chem Commun (Camb)
Year 2001
Volume (22)
Pages 2396-7
Authors Chang SC, Sommer RD, Rheingold AL, Goldberg DP
Title A model complex of a possible intermediate in the mechanism of action of peptide deformylase: first example of an (N2S)zinc(II)-formate complex.
Related PDB
Related UniProtKB
[25]
Resource
Comments
Medline ID
PubMed ID 12488004
Journal Biophys Chem
Year 2002
Volume 101-102
Pages 239-47
Authors Madison V, Duca J, Bennett F, Bohanon S, Cooper A, Chu M, Desai J, Girijavallabhan V, Hare R, Hruza A, Hendrata S, Huang Y, Kravec C, Malcolm B, McCormick J, Miesel L, Ramanathan L, Reichert P, Saksena A, Wang J, Weber PC, Zhu H, Fischmann T
Title Binding affinities and geometries of various metal ligands in peptide deformylase inhibitors.
Related PDB
Related UniProtKB
[26]
Resource
Comments
Medline ID
PubMed ID 12823970
Journal J Mol Biol
Year 2003
Volume 330
Pages 309-21
Authors Kreusch A, Spraggon G, Lee CC, Klock H, McMullan D, Ng K, Shin T, Vincent J, Warner I, Ericson C, Lesley SA
Title Structure analysis of peptide deformylases from Streptococcus pneumoniae, Staphylococcus aureus, Thermotoga maritima and Pseudomonas aeruginosa: snapshots of the oxygen sensitivity of peptide deformylase.
Related PDB
Related UniProtKB
[27]
Resource
Comments
Medline ID
PubMed ID 12924944
Journal Biochemistry
Year 2003
Volume 42
Pages 9952-8
Authors Nguyen KT, Hu X, Colton C, Chakrabarti R, Zhu MX, Pei D
Title Characterization of a human peptide deformylase: implications for antibacterial drug design.
Related PDB
Related UniProtKB
[28]
Resource
Comments
Medline ID
PubMed ID 12971750
Journal Inorg Chem
Year 2003
Volume 42
Pages 5825-36
Authors DiTargiani RC, Chang S, Salter MH Jr, Hancock RD, Goldberg DP
Title Hydrolysis of 4-Nitrophenyl Acetate by a (N(2)S(thiolate))zinc Hydroxide Complex: A Model of the Catalytically Active Intermediate for the Zinc Form of Peptide Deformylase.
Related PDB
Related UniProtKB

Comments
This enzyme belongs to the polypeptide deformylase family.
According to the literature [5] & [6], this enzyme is a Fe2+ enzyme instead of a zinc metalloprotease, showing that the zinc form is inactive.
There are a few proposed mechanism for the catalysis, raising some questions as follows:
(1) The number of the coordination of the metal involved in the catalysis, four or five: Whether the formyl carbonyl group is coordinated to the metal is still controversial.
(2) The function of Glu133: Whether this residue functions as a general base to activate the catalytic water molecule remains unclear.
As for the question (1), the papers [4] & [10] propsed a five-coordinated metal center, in which the formyl carbonyl group is coordinated to the catalytic metal, whilst the others [13] & [14] suggested a four-coordinated metal one. According to the paper [10], the state of the carbonyl carbon changes, accompanied by a transition from the four-coordinated to the five-coordinated metal center, this transition being strongly inhibited in the case of zinc form due to the tighter binding of this metal ion as compared with Fe2+ or Ni2+.
As for the question (2), in the early work on the catalysis [4], [12] & [13], Glu133 had been considered to play a dual role as a general base to activate the catalytic water, then as a general acid to protonate the leaving amide ion. However, more recently, some papers [14] & [23] suggested that Glu133 is not so critical as the general base during the catalysis, only functioning as a general acid donating the proton to the leaving group.
In any case, according to the above papers, the common feature of the catalytic mechanism is as follows:
(1) The negative charge of the carbonyl oxygen of the formyl group is stabilized by the amide of Leu91 and the sidechain of Gln50.
(2) The water or hydroxide bound to the catalytic metal (Fe2+, Ni2+ or Co2+) makes a nucleophilic attack on the carbonyl carbon that leads to a transition state (giving a four-coordinated or a five-coordinated metal center).
(3) Glu133 protonates the leaving amide group for the cleavage.

Created Updated
2003-01-27 2009-02-26