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P94462 (DEF1_BACSU) Reviewed, UniProtKB/Swiss-Prot

Last modified February 19, 2014. Version 100. 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 1

Short name=PDF 1
EC=3.5.1.88
Alternative name(s):
Polypeptide deformylase 1
Gene names
Name:defA
Synonyms:def, yloK
Ordered Locus Names:BSU15720
OrganismBacillus subtilis (strain 168) [Reference proteome] [HAMAP]
Taxonomic identifier224308 [NCBI]
Taxonomic lineageBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus

Protein attributes

Sequence length160 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
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 – 160160Peptide deformylase 1 HAMAP-Rule MF_00163
PRO_0000082739

Sites

Active site1331 By similarity
Metal binding901Iron By similarity
Metal binding1321Iron By similarity
Metal binding1361Iron By similarity

Sequences

Sequence LengthMass (Da)Tools
P94462 [UniParc].

Last modified May 1, 1997. Version 1.
Checksum: C73DBC266FDD98FC

FASTA16017,775
        10         20         30         40         50         60 
MAVKKVVTHP AEVLETPAET VTVFDKKLKK LLDDMYDTML EMDGVGLAAP QIGILKRAAV 

        70         80         90        100        110        120 
VEIGDDRGRI DLVNPEILEK SGEQTGIEGC LSFPNVYGDV TRADYVKVRA FNRQGKPFIL 

       130        140        150        160 
EARGFLARAV QHEMDHLDGV LFTSKISKYY TEDELADMEG 

« Hide

References

« Hide 'large scale' references
[1]"A survey of polypeptide deformylase function throughout the eubacterial lineage."
Mazel D., Coic E., Blanchard S., Saurin W., Marliere P.
J. Mol. Biol. 266:939-949(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: 168.
[2]"A 28 kbp segment from the spoVM region of the Bacillus subtilis 168 genome."
Foulger D., Errington J.
Microbiology 144:801-805(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: 168.
[3]"The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V. expand/collapse author list , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: 168.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
Y10304 Genomic DNA. Translation: CAA71349.1.
Y13937 Genomic DNA. Translation: CAA74262.1.
AL009126 Genomic DNA. Translation: CAB13445.1.
PIRF69613.
RefSeqNP_389454.1. NC_000964.3.

3D structure databases

ProteinModelPortalP94462.
SMRP94462. Positions 1-150.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING224308.BSU15720.

Proteomic databases

PaxDbP94462.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaCAB13445; CAB13445; BSU15720.
GeneID938819.
KEGGbsu:BSU15720.
PATRIC18974951. VBIBacSub10457_1667.

Organism-specific databases

GenoListBSU15720. [Micado]

Phylogenomic databases

eggNOGCOG0242.
HOGENOMHOG000243509.
KOK01462.
OMAPIGEDIQ.
OrthoDBEOG664CMF.
ProtClustDBPRK12846.

Enzyme and pathway databases

BioCycBSUB:BSU15720-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...

Entry information

Entry nameDEF1_BACSU
AccessionPrimary (citable) accession number: P94462
Entry history
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: May 1, 1997
Last modified: February 19, 2014
This is version 100 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

Bacillus subtilis

Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList