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Protein

Peptide deformylase

Gene

def

Organism
Azotobacter vinelandii (strain DJ / ATCC BAA-1303)
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

BioCyciAVIN322710:GJ0M-17-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Peptide deformylaseUniRule annotation (EC:3.5.1.88UniRule annotation)
Short name:
PDFUniRule annotation
Alternative name(s):
Polypeptide deformylaseUniRule annotation
Gene namesi
Name:defUniRule annotation
Ordered Locus Names:Avin_00170
OrganismiAzotobacter vinelandii (strain DJ / ATCC BAA-1303)
Taxonomic identifieri322710 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaeAzotobacter
ProteomesiUP000002424: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 168168Peptide deformylasePRO_1000203599Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi322710.Avin_00170.

Structurei

3D structure databases

ProteinModelPortaliC1DFV8.
SMRiC1DFV8. Positions 1-167.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
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.

C1DFV8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAILTILEFP DPRLRTIAKP IETVDDGIRR LIDDMFETMY AAPGIGLAAT
60 70 80 90 100
QVNVHKRLVV MDLSEDKNEP RVFINPEFEA LTEELEPYQE GCLSVPGFYE
110 120 130 140 150
NVDRPQKVRI RALDRDGQPF ELVAEGLLAV CIQHECDHLN GKLFVDYLST
160
LKRDRIRKKL EKQHRQHG
Length:168
Mass (Da):19,339
Last modified:May 26, 2009 - v1
Checksum:i814A448CFDFEB8C2
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001157 Genomic DNA. Translation: ACO76285.1.
RefSeqiYP_002797260.1. NC_012560.1.

Genome annotation databases

EnsemblBacteriaiACO76285; ACO76285; Avin_00170.
GeneIDi7758985.
KEGGiavn:Avin_00170.
PATRICi21026420. VBIAzoVin72790_0017.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001157 Genomic DNA. Translation: ACO76285.1.
RefSeqiYP_002797260.1. NC_012560.1.

3D structure databases

ProteinModelPortaliC1DFV8.
SMRiC1DFV8. Positions 1-167.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi322710.Avin_00170.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACO76285; ACO76285; Avin_00170.
GeneIDi7758985.
KEGGiavn:Avin_00170.
PATRICi21026420. VBIAzoVin72790_0017.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiFDTMYEE.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciAVIN322710:GJ0M-17-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: DJ / ATCC BAA-1303.

Entry informationi

Entry nameiDEF_AZOVD
AccessioniPrimary (citable) accession number: C1DFV8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 22, 2009
Last sequence update: May 26, 2009
Last modified: January 7, 2015
This is version 37 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.