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Protein

Peptide deformylase

Gene

def

Organism
Wolinella succinogenes (strain ATCC 29543 / DSM 1740 / LMG 7466 / NCTC 11488 / FDC 602W) (Vibrio succinogenes)
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 bindingi94 – 941IronUniRule annotation
Metal bindingi136 – 1361IronUniRule annotation
Active sitei137 – 1371UniRule annotation
Metal bindingi140 – 1401IronUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

Iron, Metal-binding

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:WS2212
OrganismiWolinella succinogenes (strain ATCC 29543 / DSM 1740 / LMG 7466 / NCTC 11488 / FDC 602W) (Vibrio succinogenes)
Taxonomic identifieri273121 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaEpsilonproteobacteriaCampylobacteralesHelicobacteraceaeWolinella
ProteomesiUP000000422 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 170170Peptide deformylasePRO_0000082882Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi273121.WS2212.

Structurei

3D structure databases

ProteinModelPortaliQ7M7M2.
SMRiQ7M7M2. Positions 1-164.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiSFDSKLH.
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.

Q7M7M2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLPIITYPHP LLKKRSEPVT LFDEELRQFL DEMYITMLAK NGVGLAAVQV
60 70 80 90 100
GNPIRALIVN IPDEEGNQER ENLLEIINPE FLSKEGEIQF NEGCLSVPEF
110 120 130 140 150
YEDVTRFDRV RLTYQDRYGE RHEIEAEGYL AVALQHEIDH LNGILFIDKL
160 170
SLIKRKKFEK ELKKRQRASL
Length:170
Mass (Da):19,841
Last modified:December 15, 2003 - v1
Checksum:i41D06712686ABA3B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BX571663 Genomic DNA. Translation: CAE11201.1.
RefSeqiWP_011139983.1. NC_005090.1.

Genome annotation databases

EnsemblBacteriaiCAE11201; CAE11201; WS2212.
KEGGiwsu:WS2212.
PATRICi24041344. VBIWolSuc63014_2082.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BX571663 Genomic DNA. Translation: CAE11201.1.
RefSeqiWP_011139983.1. NC_005090.1.

3D structure databases

ProteinModelPortaliQ7M7M2.
SMRiQ7M7M2. Positions 1-164.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi273121.WS2212.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAE11201; CAE11201; WS2212.
KEGGiwsu:WS2212.
PATRICi24041344. VBIWolSuc63014_2082.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiSFDSKLH.
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.
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 29543 / DSM 1740 / LMG 7466 / NCTC 11488 / FDC 602W.

Entry informationi

Entry nameiDEF_WOLSU
AccessioniPrimary (citable) accession number: Q7M7M2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 2003
Last sequence update: December 15, 2003
Last modified: July 22, 2015
This is version 70 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.