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Protein

Peptide deformylase

Gene

def

Organism
Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
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 (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 bindingi96 – 961IronBy similarity
Metal bindingi138 – 1381IronBy similarity
Active sitei139 – 1391By similarity
Metal bindingi142 – 1421IronBy 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

BioCyciHPY:HP0793-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Peptide deformylase (EC:3.5.1.88)
Short name:
PDF
Alternative name(s):
Polypeptide deformylase
Gene namesi
Name:def
Ordered Locus Names:HP_0793
OrganismiHelicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
Taxonomic identifieri85962 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaEpsilonproteobacteriaCampylobacteralesHelicobacteraceaeHelicobacter
ProteomesiUP000000429 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 174174Peptide deformylasePRO_0000082790Add
BLAST

Proteomic databases

PRIDEiP56419.

Interactioni

Protein-protein interaction databases

DIPiDIP-3266N.
IntActiP56419. 5 interactions.
MINTiMINT-165640.
STRINGi85962.HP0793.

Structurei

3D structure databases

ProteinModelPortaliP56419.
SMRiP56419. Positions 2-167.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.Curated

Phylogenomic databases

eggNOGiCOG0242.
KOiK01462.
OMAiLEIIHYP.
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.

P56419-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MALLEIIHYP SKILRTISKE VVSFDSKLHQ QLDDMHETMI ASEGIGLAAI
60 70 80 90 100
QVGLPLRMLI INLPQEDGVQ HKEDCLEIIN PKFIETGGSM MYREGCLSVP
110 120 130 140 150
GFYEEVERFE KVKIEYQNRF AEVKVLEASE LLAVAIQHEI DHLNGVLFVD
160 170
KLSILKRKKF EKELKELQKK QKHE
Length:174
Mass (Da):20,057
Last modified:July 15, 1998 - v1
Checksum:i375525F45E5CC774
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000511 Genomic DNA. Translation: AAD07841.1.
PIRiA64619.
RefSeqiNP_207586.1. NC_000915.1.
WP_001185845.1. NC_018939.1.
YP_006934707.1. NC_018939.1.

Genome annotation databases

EnsemblBacteriaiAAD07841; AAD07841; HP_0793.
GeneIDi899348.
KEGGiheo:C694_04065.
hpy:HP0793.
PATRICi20592873. VBIHelPyl33062_0825.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000511 Genomic DNA. Translation: AAD07841.1.
PIRiA64619.
RefSeqiNP_207586.1. NC_000915.1.
WP_001185845.1. NC_018939.1.
YP_006934707.1. NC_018939.1.

3D structure databases

ProteinModelPortaliP56419.
SMRiP56419. Positions 2-167.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-3266N.
IntActiP56419. 5 interactions.
MINTiMINT-165640.
STRINGi85962.HP0793.

Proteomic databases

PRIDEiP56419.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAD07841; AAD07841; HP_0793.
GeneIDi899348.
KEGGiheo:C694_04065.
hpy:HP0793.
PATRICi20592873. VBIHelPyl33062_0825.

Phylogenomic databases

eggNOGiCOG0242.
KOiK01462.
OMAiLEIIHYP.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciHPY:HP0793-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: ATCC 700392 / 26695.

Entry informationi

Entry nameiDEF_HELPY
AccessioniPrimary (citable) accession number: P56419
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: July 15, 1998
Last modified: May 27, 2015
This is version 95 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. Helicobacter pylori
    Helicobacter pylori (strain 26695): entries and gene names
  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.