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Protein

Peptide deformylase

Gene

def

Organism
Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai (strain 56601)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions (By similarity).By similarity

Catalytic activityi

Formyl-L-methionyl peptide + H2O = formate + methionyl peptide.

Cofactori

Fe2+By similarityNote: Binds 1 Fe2+ ion.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi102 – 1021IronBy similarity
Metal bindingi144 – 1441IronBy similarity
Active sitei145 – 1451By similarity
Metal bindingi148 – 1481IronBy similarity

GO - Molecular functioni

  1. iron ion binding Source: InterPro
  2. peptide deformylase activity Source: UniProtKB-HAMAP

GO - Biological processi

  1. translation Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

Iron, Metal-binding

Enzyme and pathway databases

BioCyciLINT189518:GJBB-1994-MONOMER.
BRENDAi3.5.1.88. 2986.

Names & Taxonomyi

Protein namesi
Recommended name:
Peptide deformylase (EC:3.5.1.88)
Short name:
PDF
Alternative name(s):
Polypeptide deformylase
Gene namesi
Name:def
Synonyms:pdf
Ordered Locus Names:LA_2438
OrganismiLeptospira interrogans serogroup Icterohaemorrhagiae serovar Lai (strain 56601)
Taxonomic identifieri189518 [NCBI]
Taxonomic lineageiBacteriaSpirochaetesSpirochaetalesLeptospiraceaeLeptospira
ProteomesiUP000001408 Componenti: Chromosome I

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 178178Peptide deformylasePRO_0000082795Add
BLAST

Proteomic databases

PaxDbiQ93LE9.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

STRINGi189518.LA2438.

Structurei

Secondary structure

1
178
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi12 – 154Combined sources
Helixi23 – 253Combined sources
Helixi29 – 4416Combined sources
Beta strandi48 – 514Combined sources
Helixi52 – 554Combined sources
Beta strandi59 – 646Combined sources
Beta strandi70 – 723Combined sources
Beta strandi81 – 9010Combined sources
Beta strandi95 – 1028Combined sources
Beta strandi105 – 12319Combined sources
Beta strandi129 – 1357Combined sources
Helixi136 – 14914Combined sources
Helixi154 – 1574Combined sources
Beta strandi163 – 1664Combined sources
Helixi167 – 1737Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1SV2X-ray3.00A/B2-178[»]
1SZZX-ray3.30A/B/C/D/E/F/G/H2-178[»]
1VEVX-ray2.51A/B2-178[»]
1VEYX-ray3.30A/B2-178[»]
1VEZX-ray2.30A/B2-178[»]
1Y6HX-ray2.20A/B2-178[»]
SMRiQ93LE9. Positions 2-178.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ93LE9.

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.Curated

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243508.
InParanoidiQ93LE9.
KOiK01462.
OMAiLEIIHYP.
OrthoDBiEOG664CMF.

Family and domain databases

Gene3Di3.90.45.10. 1 hit.
HAMAPiMF_00163. Pep_deformylase.
InterProiIPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view]
PANTHERiPTHR10458. PTHR10458. 1 hit.
PfamiPF01327. Pep_deformylase. 1 hit.
[Graphical view]
PIRSFiPIRSF004749. Pep_def. 1 hit.
PRINTSiPR01576. PDEFORMYLASE.
SUPFAMiSSF56420. SSF56420. 1 hit.
TIGRFAMsiTIGR00079. pept_deformyl. 1 hit.

Sequencei

Sequence statusi: Complete.

Q93LE9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSVRKILRMG DPILRKISEP VTEDEIQTKE FKKLIRDMFD TMRHAEGVGL
60 70 80 90 100
AAPQIGILKQ IVVVGSEDNE RYPGTPDVPE RIILNPVITP LTKDTSGFWE
110 120 130 140 150
GCLSVPGMRG YVERPNQIRM QWMDEKGNQF DETIDGYKAI VYQHECDHLQ
160 170
GILYVDRLKD TKLFGFNETL DSSHNVLD
Length:178
Mass (Da):20,379
Last modified:November 30, 2001 - v1
Checksum:i8F6F3D2449A48B10
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY040678 Genomic DNA. Translation: AAK70806.1.
AE010300 Genomic DNA. Translation: AAN49637.1.
RefSeqiNP_712619.1. NC_004342.2.
WP_000116243.1. NC_004342.2.

Genome annotation databases

EnsemblBacteriaiAAN49637; AAN49637; LA_2438.
GeneIDi1151781.
KEGGilil:LA_2438.
PATRICi22385704. VBILepInt91350_2418.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY040678 Genomic DNA. Translation: AAK70806.1.
AE010300 Genomic DNA. Translation: AAN49637.1.
RefSeqiNP_712619.1. NC_004342.2.
WP_000116243.1. NC_004342.2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1SV2X-ray3.00A/B2-178[»]
1SZZX-ray3.30A/B/C/D/E/F/G/H2-178[»]
1VEVX-ray2.51A/B2-178[»]
1VEYX-ray3.30A/B2-178[»]
1VEZX-ray2.30A/B2-178[»]
1Y6HX-ray2.20A/B2-178[»]
SMRiQ93LE9. Positions 2-178.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi189518.LA2438.

Proteomic databases

PaxDbiQ93LE9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAN49637; AAN49637; LA_2438.
GeneIDi1151781.
KEGGilil:LA_2438.
PATRICi22385704. VBILepInt91350_2418.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243508.
InParanoidiQ93LE9.
KOiK01462.
OMAiLEIIHYP.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciLINT189518:GJBB-1994-MONOMER.
BRENDAi3.5.1.88. 2986.

Miscellaneous databases

EvolutionaryTraceiQ93LE9.

Family and domain databases

Gene3Di3.90.45.10. 1 hit.
HAMAPiMF_00163. Pep_deformylase.
InterProiIPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view]
PANTHERiPTHR10458. PTHR10458. 1 hit.
PfamiPF01327. Pep_deformylase. 1 hit.
[Graphical view]
PIRSFiPIRSF004749. Pep_def. 1 hit.
PRINTSiPR01576. PDEFORMYLASE.
SUPFAMiSSF56420. SSF56420. 1 hit.
TIGRFAMsiTIGR00079. pept_deformyl. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning, high-level expression, purification and crystallization of peptide deformylase from Leptospira interrogans."
    Li Y., Ren S., Gong W.
    Acta Crystallogr. D 58:846-848(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CRYSTALLIZATION.
    Strain: Lai / Serogroup Icterohaemorrhagiae / Serovar lai.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 56601.
  3. "Unique structural characteristics of peptide deformylase from pathogenic bacterium Leptospira interrogans."
    Zhou Z., Song X., Li Y., Gong W.
    J. Mol. Biol. 339:207-215(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS), SUBUNIT.
    Strain: Lai / Serogroup Icterohaemorrhagiae / Serovar lai.

Entry informationi

Entry nameiDEF_LEPIN
AccessioniPrimary (citable) accession number: Q93LE9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 18, 2002
Last sequence update: November 30, 2001
Last modified: March 31, 2015
This is version 90 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.