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Protein

Peptide deformylase

Gene

def

Organism
Helicobacter pylori (strain Shi470)
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 bindingi96 – 961IronUniRule annotation
Metal bindingi138 – 1381IronUniRule annotation
Active sitei139 – 1391UniRule annotation
Metal bindingi142 – 1421IronUniRule 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

BioCyciHPYL512562:GHHZ-572-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:HPSH_02850
OrganismiHelicobacter pylori (strain Shi470)
Taxonomic identifieri512562 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaEpsilonproteobacteriaCampylobacteralesHelicobacteraceaeHelicobacter
ProteomesiUP000008831: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 175175Peptide deformylasePRO_1000097316Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi512562.HPSH_02850.

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
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.

B2UT38-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MALLEIIHYP SKILRTISKE IVSFDSKLHQ QLDDMRETMI ASEGIGLAAI
60 70 80 90 100
QVGLPLRMLI INLPREDGVQ HKEDCLEIIN PKFIETKGTI MYKEGCLSVP
110 120 130 140 150
GFYEEVERFE KVKIEYQNRF AEVKVLEASE LLAVAIQHEI DHLNGVLFVD
160 170
KLSILKRKKF EKELKELNKN PKSKS
Length:175
Mass (Da):20,135
Last modified:July 1, 2008 - v1
Checksum:i96A48D503239A4CA
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001072 Genomic DNA. Translation: ACD48020.1.
RefSeqiWP_001185796.1. NC_010698.2.
YP_001910050.1. NC_010698.2.

Genome annotation databases

EnsemblBacteriaiACD48020; ACD48020; HPSH_02850.
GeneIDi6296082.
KEGGihps:HPSH_02850.
PATRICi20612489. VBIHelPyl23559_0556.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001072 Genomic DNA. Translation: ACD48020.1.
RefSeqiWP_001185796.1. NC_010698.2.
YP_001910050.1. NC_010698.2.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi512562.HPSH_02850.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACD48020; ACD48020; HPSH_02850.
GeneIDi6296082.
KEGGihps:HPSH_02850.
PATRICi20612489. VBIHelPyl23559_0556.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiLEIIHYP.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciHPYL512562:GHHZ-572-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. "Genome sequence of Helicobacter pylori from the remote Amazon: traces of Asian ancestry of the first Americans."
    Kersulyte D., Kalia A., Gilman R.H., Berg D.E.
    Submitted (MAY-2008) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Shi470.

Entry informationi

Entry nameiDEF_HELPS
AccessioniPrimary (citable) accession number: B2UT38
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: July 1, 2008
Last modified: February 4, 2015
This is version 45 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

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.