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Protein

Peptide deformylase 1

Gene

def1

Organism
Pseudomonas putida (strain KT2440)
Status
Reviewed-Annotation score: Annotation score: 2 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.UniRule annotation

Catalytic activityi

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

Cofactori

Fe2+UniRule annotationNote: Binds 1 Fe2+ ion.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi92 – 921IronUniRule annotation
Metal bindingi134 – 1341IronUniRule annotation
Active sitei135 – 1351UniRule annotation
Metal bindingi138 – 1381IronUniRule annotation

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

BioCyciPPUT160488:GIXO-68-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Peptide deformylase 1UniRule annotation (EC:3.5.1.88UniRule annotation)
Short name:
PDF 1UniRule annotation
Alternative name(s):
Polypeptide deformylase 1UniRule annotation
Gene namesi
Name:def1UniRule annotation
Ordered Locus Names:PP_0068
OrganismiPseudomonas putida (strain KT2440)
Taxonomic identifieri160488 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas
ProteomesiUP000000556 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 168168Peptide deformylase 1PRO_0000082820Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi160488.PP_0068.

Structurei

3D structure databases

ProteinModelPortaliQ88RR1.
SMRiQ88RR1. Positions 2-168.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243508.
KOiK01462.
OMAiFDTMYEE.
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.

Q88RR1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAILNILEFP DPRLRTLAKP VTEFDDALRQ LIDDMFETMY EAPGIGLAAT
60 70 80 90 100
QVNVHKQVVV MDLSEDRSEP RVFINPSVEE LTHDMGQYQE GCLSVPGFYE
110 120 130 140 150
NVDRPLRVRV KAQDRDGKPF ELECEGLLAV CVQHEFDHLN GKLFVDYLSQ
160
LKRDRIKKKL EKQHRQQA
Length:168
Mass (Da):19,410
Last modified:June 1, 2003 - v1
Checksum:i8E550C63A77F0130
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE015451 Genomic DNA. Translation: AAN65702.1.
RefSeqiNP_742238.1. NC_002947.3.

Genome annotation databases

EnsemblBacteriaiAAN65702; AAN65702; PP_0068.
GeneIDi1043549.
KEGGippu:PP_0068.
PATRICi19938108. VBIPsePut30601_0073.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE015451 Genomic DNA. Translation: AAN65702.1.
RefSeqiNP_742238.1. NC_002947.3.

3D structure databases

ProteinModelPortaliQ88RR1.
SMRiQ88RR1. Positions 2-168.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi160488.PP_0068.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAN65702; AAN65702; PP_0068.
GeneIDi1043549.
KEGGippu:PP_0068.
PATRICi19938108. VBIPsePut30601_0073.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243508.
KOiK01462.
OMAiFDTMYEE.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciPPUT160488:GIXO-68-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

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: KT2440.

Entry informationi

Entry nameiDEF1_PSEPK
AccessioniPrimary (citable) accession number: Q88RR1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 27, 2003
Last sequence update: June 1, 2003
Last modified: January 7, 2015
This is version 73 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. 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.