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Protein

Peptide deformylase

Gene

def

Organism
Helicobacter hepaticus (strain ATCC 51449 / 3B1)
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 bindingi104 – 1041IronUniRule annotation
Metal bindingi146 – 1461IronUniRule annotation
Active sitei147 – 1471UniRule annotation
Metal bindingi150 – 1501IronUniRule 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

BioCyciHHEP235279:GHUA-587-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:HH_0569
OrganismiHelicobacter hepaticus (strain ATCC 51449 / 3B1)
Taxonomic identifieri235279 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaEpsilonproteobacteriaCampylobacteralesHelicobacteraceaeHelicobacter
ProteomesiUP000002495 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 181181Peptide deformylasePRO_0000082789Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi235279.HH0569.

Structurei

3D structure databases

ProteinModelPortaliQ7VIN5.
SMRiQ7VIN5. Positions 9-175.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
KOiK01462.
OMAiIEYYDEN.
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.

Q7VIN5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKYPEMTLAT LAILKYPNAL LRKKSIPVEI FDDNLHNFLD DMYETLIESK
60 70 80 90 100
GVGLAAIQVG RAERILIINI PREEDKQQYK EDLLEIINPT FLTQEECVEW
110 120 130 140 150
EEGCLSVPDF YESIKRFDKV SIAYKDRYGN DRILKAQGFL AVAIQHEIDH
160 170 180
LNGVLFVDKL PILKRKKFEK ELKKLKKESQ A
Length:181
Mass (Da):21,072
Last modified:September 30, 2003 - v1
Checksum:i9A4ABE10E455EB8D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE017125 Genomic DNA. Translation: AAP77166.1.
RefSeqiNP_860100.1. NC_004917.1.
WP_011115411.1. NC_004917.1.

Genome annotation databases

EnsemblBacteriaiAAP77166; AAP77166; HH_0569.
KEGGihhe:HH0569.
PATRICi20588594. VBIHelHep90276_0574.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE017125 Genomic DNA. Translation: AAP77166.1.
RefSeqiNP_860100.1. NC_004917.1.
WP_011115411.1. NC_004917.1.

3D structure databases

ProteinModelPortaliQ7VIN5.
SMRiQ7VIN5. Positions 9-175.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi235279.HH0569.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAP77166; AAP77166; HH_0569.
KEGGihhe:HH0569.
PATRICi20588594. VBIHelHep90276_0574.

Phylogenomic databases

eggNOGiCOG0242.
KOiK01462.
OMAiIEYYDEN.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciHHEP235279:GHUA-587-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 51449 / 3B1.

Entry informationi

Entry nameiDEF_HELHP
AccessioniPrimary (citable) accession number: Q7VIN5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 14, 2003
Last sequence update: September 30, 2003
Last modified: March 31, 2015
This is version 71 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.