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Q93LE9 (DEF_LEPIN) Reviewed, UniProtKB/Swiss-Prot

Last modified February 19, 2014. Version 83. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Peptide deformylase

Short name=PDF
EC=3.5.1.88
Alternative name(s):
Polypeptide deformylase
Gene names
Name:def
Synonyms:pdf
Ordered Locus Names:LA_2438
OrganismLeptospira interrogans serogroup Icterohaemorrhagiae serovar Lai (strain 56601) [Reference proteome] [HAMAP]
Taxonomic identifier189518 [NCBI]
Taxonomic lineageBacteriaSpirochaetesSpirochaetalesLeptospiraceaeLeptospira

Protein attributes

Sequence length178 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. HAMAP-Rule MF_00163

Catalytic activity

Formyl-L-methionyl peptide + H2O = formate + methionyl peptide. HAMAP-Rule MF_00163

Cofactor

Binds 1 Fe2+ ion By similarity. HAMAP-Rule MF_00163

Subunit structure

Homodimer. Ref.3

Sequence similarities

Belongs to the polypeptide deformylase family.

Ontologies

Keywords
   Biological processProtein biosynthesis
   LigandIron
Metal-binding
   Molecular functionHydrolase
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processtranslation

Inferred from electronic annotation. Source: UniProtKB-HAMAP

   Molecular_functioniron ion binding

Inferred from electronic annotation. Source: InterPro

peptide deformylase activity

Inferred from electronic annotation. Source: UniProtKB-HAMAP

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 178178Peptide deformylase HAMAP-Rule MF_00163
PRO_0000082795

Sites

Active site1451 By similarity
Metal binding1021Iron By similarity
Metal binding1441Iron By similarity
Metal binding1481Iron By similarity

Secondary structure

............................ 178
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q93LE9 [UniParc].

Last modified December 1, 2001. Version 1.
Checksum: 8F6F3D2449A48B10

FASTA17820,379
        10         20         30         40         50         60 
MSVRKILRMG DPILRKISEP VTEDEIQTKE FKKLIRDMFD TMRHAEGVGL AAPQIGILKQ 

        70         80         90        100        110        120 
IVVVGSEDNE RYPGTPDVPE RIILNPVITP LTKDTSGFWE GCLSVPGMRG YVERPNQIRM 

       130        140        150        160        170 
QWMDEKGNQF DETIDGYKAI VYQHECDHLQ GILYVDRLKD TKLFGFNETL DSSHNVLD 

« Hide

References

« Hide 'large scale' references
[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(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CRYSTALLIZATION.
Strain: Lai / Serogroup Icterohaemorrhagiae / Serovar lai.
[2]"Unique physiological and pathogenic features of Leptospira interrogans revealed by whole-genome sequencing."
Ren S.-X., Fu G., Jiang X.-G., Zeng R., Miao Y.-G., Xu H., Zhang Y.-X., Xiong H., Lu G., Lu L.-F., Jiang H.-Q., Jia J., Tu Y.-F., Jiang J.-X., Gu W.-Y., Zhang Y.-Q., Cai Z., Sheng H.-H. expand/collapse author list , Yin H.-F., Zhang Y., Zhu G.-F., Wan M., Huang H.-L., Qian Z., Wang S.-Y., Ma W., Yao Z.-J., Shen Y., Qiang B.-Q., Xia Q.-C., Guo X.-K., Danchin A., Saint Girons I., Somerville R.L., Wen Y.-M., Shi M.-H., Chen Z., Xu J.-G., Zhao G.-P.
Nature 422:888-893(2003) [PubMed] [Europe PMC] [Abstract]
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(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS), SUBUNIT.
Strain: Lai / Serogroup Icterohaemorrhagiae / Serovar lai.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AY040678 Genomic DNA. Translation: AAK70806.1.
AE010300 Genomic DNA. Translation: AAN49637.1.
RefSeqNP_712619.1. NC_004342.2.

3D structure databases

PDBe
RCSB PDB
PDBj
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[»]
ProteinModelPortalQ93LE9.
SMRQ93LE9. Positions 2-178.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING189518.LA2438.

Proteomic databases

PaxDbQ93LE9.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAN49637; AAN49637; LA_2438.
GeneID1151781.
KEGGlil:LA_2438.
PATRIC22385704. VBILepInt91350_2418.

Phylogenomic databases

eggNOGCOG0242.
HOGENOMHOG000243508.
KOK01462.
OMALETMYQA.
OrthoDBEOG664CMF.
ProtClustDBPRK12846.

Enzyme and pathway databases

BioCycLINT189518:GJBB-1994-MONOMER.

Family and domain databases

Gene3D3.90.45.10. 1 hit.
HAMAPMF_00163. Pep_deformylase.
InterProIPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view]
PANTHERPTHR10458. PTHR10458. 1 hit.
PfamPF01327. Pep_deformylase. 1 hit.
[Graphical view]
PIRSFPIRSF004749. Pep_def. 1 hit.
PRINTSPR01576. PDEFORMYLASE.
SUPFAMSSF56420. SSF56420. 1 hit.
TIGRFAMsTIGR00079. pept_deformyl. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceQ93LE9.

Entry information

Entry nameDEF_LEPIN
AccessionPrimary (citable) accession number: Q93LE9
Entry history
Integrated into UniProtKB/Swiss-Prot: September 19, 2002
Last sequence update: December 1, 2001
Last modified: February 19, 2014
This is version 83 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references