Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Peptide deformylase 1

Gene

defA

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

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 bindingi90 – 901IronBy similarity
Metal bindingi132 – 1321IronBy similarity
Active sitei133 – 1331By similarity
Metal bindingi136 – 1361IronBy similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

Iron, Metal-binding

Enzyme and pathway databases

BioCyciBSUB:BSU15720-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Peptide deformylase 1 (EC:3.5.1.88)
Short name:
PDF 1
Alternative name(s):
Polypeptide deformylase 1
Gene namesi
Name:defA
Synonyms:def, yloK
Ordered Locus Names:BSU15720
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
ProteomesiUP000001570 Componenti: Chromosome

Organism-specific databases

GenoListiBSU15720. [Micado]

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 160160Peptide deformylase 1PRO_0000082739Add
BLAST

Proteomic databases

PaxDbiP94462.

Interactioni

Protein-protein interaction databases

IntActiP94462. 1 interaction.
STRINGi224308.Bsubs1_010100008681.

Structurei

3D structure databases

ProteinModelPortaliP94462.
SMRiP94462. Positions 1-150.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.Curated

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
InParanoidiP94462.
KOiK01462.
OMAiSFDSKLH.
OrthoDBiEOG664CMF.
PhylomeDBiP94462.

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.

P94462-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAVKKVVTHP AEVLETPAET VTVFDKKLKK LLDDMYDTML EMDGVGLAAP
60 70 80 90 100
QIGILKRAAV VEIGDDRGRI DLVNPEILEK SGEQTGIEGC LSFPNVYGDV
110 120 130 140 150
TRADYVKVRA FNRQGKPFIL EARGFLARAV QHEMDHLDGV LFTSKISKYY
160
TEDELADMEG
Length:160
Mass (Da):17,775
Last modified:May 1, 1997 - v1
Checksum:iC73DBC266FDD98FC
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y10304 Genomic DNA. Translation: CAA71349.1.
Y13937 Genomic DNA. Translation: CAA74262.1.
AL009126 Genomic DNA. Translation: CAB13445.1.
PIRiF69613.
RefSeqiNP_389454.1. NC_000964.3.
WP_003232077.1. NZ_JNCM01000035.1.

Genome annotation databases

EnsemblBacteriaiCAB13445; CAB13445; BSU15720.
GeneIDi938819.
KEGGibsu:BSU15720.
PATRICi18974951. VBIBacSub10457_1667.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y10304 Genomic DNA. Translation: CAA71349.1.
Y13937 Genomic DNA. Translation: CAA74262.1.
AL009126 Genomic DNA. Translation: CAB13445.1.
PIRiF69613.
RefSeqiNP_389454.1. NC_000964.3.
WP_003232077.1. NZ_JNCM01000035.1.

3D structure databases

ProteinModelPortaliP94462.
SMRiP94462. Positions 1-150.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP94462. 1 interaction.
STRINGi224308.Bsubs1_010100008681.

Proteomic databases

PaxDbiP94462.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB13445; CAB13445; BSU15720.
GeneIDi938819.
KEGGibsu:BSU15720.
PATRICi18974951. VBIBacSub10457_1667.

Organism-specific databases

GenoListiBSU15720. [Micado]

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
InParanoidiP94462.
KOiK01462.
OMAiSFDSKLH.
OrthoDBiEOG664CMF.
PhylomeDBiP94462.

Enzyme and pathway databases

BioCyciBSUB:BSU15720-MONOMER.

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. "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.
    , 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.

Entry informationi

Entry nameiDEF1_BACSU
AccessioniPrimary (citable) accession number: P94462
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: May 1, 1997
Last modified: July 22, 2015
This is version 109 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

Complete proteome, Reference proteome

Documents

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