Skip Header

Contribute Send feedback
Read comments (?) or add your own

Q04RW4 (DEF_LEPBJ) Reviewed, UniProtKB/Swiss-Prot

Last modified May 29, 2013. Version 43. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (1) | 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
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
Ordered Locus Names:LBJ_1823
OrganismLeptospira borgpetersenii serovar Hardjo-bovis (strain JB197) [Complete proteome] [HAMAP]
Taxonomic identifier355277 [NCBI]
Taxonomic lineageBacteria › Spirochaetes › Spirochaetales › Leptospiraceae › Leptospira ›

Protein attributes

Sequence length178 AA.
Sequence statusComplete.
Protein existenceInferred from homology

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

Sequence similarities

Belongs to the polypeptide deformylase family.

Ontologies

Keywords
   Biological processProtein biosynthesis
   LigandIron
Metal-binding
   Molecular functionHydrolase
   Technical termComplete proteome
Gene Ontology (GO)
   Biological_processtranslation

Inferred from electronic annotation. Source: HAMAP

   Molecular_functioniron ion binding

Inferred from electronic annotation. Source: InterPro

peptide deformylase activity

Inferred from electronic annotation. Source: HAMAP

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 178178Peptide deformylase HAMAP-Rule MF_00163
PRO_0000301050

Sites

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

Sequences

Sequence LengthMass (Da)Tools
Q04RW4 [UniParc].

Last modified November 14, 2006. Version 1.
Checksum: EC1415F75FE9E42C

FASTA17820,344
        10         20         30         40         50         60 
MSVRKILRMG DSILRQVSIP VTENELQTKE FKKLIRDMFD TMRHAEGVGL AAPQIGILKQ 

        70         80         90        100        110        120 
IVVVGSEDNE RYPDTPNVPE RVILNPIITP LTKDTSGFWE GCLSVPGMRG YVERPNKIRM 

       130        140        150        160        170 
QWMDEKGDRF DETIDGYKAV VYQHECDHLS GILYVDRLKD TKLFGFNDTL DSGRNVLD

« Hide

References

[1]"Genome reduction in Leptospira borgpetersenii reflects limited transmission potential."
Bulach D.M., Zuerner R.L., Wilson P., Seemann T., McGrath A., Cullen P.A., Davis J., Johnson M., Kuczek E., Alt D.P., Peterson-Burch B., Coppel R.L., Rood J.I., Davies J.K., Adler B.
Proc. Natl. Acad. Sci. U.S.A. 103:14560-14565(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: JB197.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		CP000350 Genomic DNA. Translation: ABJ76356.1.
RefSeqYP_801114.1. NC_008510.1.

3D structure databases

ProteinModelPortalQ04RW4.
SMRQ04RW4. Positions 2-178.
ModBaseSearch...

Protein-protein interaction databases

STRING355277.LBJ_1823.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaABJ76356; ABJ76356; LBJ_1823.
GeneID4410339.
KEGGlbj:LBJ_1823.
PATRIC22359265. VBILepBor13265_2341.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0242.
HOGENOMHOG000243508.
KOK01462.
OMARFADGFH.
ProtClustDBPRK12846.

Enzyme and pathway databases

BioCycLBOR355277:GHYM-1801-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. Fmet_deformylase. 1 hit.
TIGRFAMsTIGR00079. pept_deformyl. 1 hit.
ProtoNetSearch...

Entry information

Entry nameDEF_LEPBJ
AccessionPrimary (citable) accession number: Q04RW4
Entry history
Integrated into UniProtKB/Swiss-Prot: September 11, 2007
Last sequence update: November 14, 2006
Last modified: May 29, 2013
This is version 43 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

to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents