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Protein

Peptide deformylase

Gene

def

Organism
Hyphomonas neptunium (strain ATCC 15444)
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 bindingi95 – 951IronUniRule annotation
Metal bindingi137 – 1371IronUniRule annotation
Active sitei138 – 1381UniRule annotation
Metal bindingi141 – 1411IronUniRule annotation

GO - Molecular functioni

  1. iron ion binding Source: InterPro
  2. peptide deformylase activity Source: JCVI

GO - Biological processi

  1. cellular protein modification process Source: JCVI
  2. 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

BioCyciHNEP228405:GI69-512-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:HNE_0512
OrganismiHyphomonas neptunium (strain ATCC 15444)
Taxonomic identifieri228405 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhodobacteralesHyphomonadaceaeHyphomonas
ProteomesiUP000001959 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 176176Peptide deformylasePRO_0000301040Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi228405.HNE_0512.

Structurei

3D structure databases

ProteinModelPortaliQ0C4V1.
SMRiQ0C4V1. Positions 2-167.
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.

Q0C4V1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAIREILTVP DPRLKQVSKP VEGGVTDDIR ALMDDMLETM YDAPGIGLAA
60 70 80 90 100
IQIGVPLRVI VMDLAREGEE PAPRYFVNPE ILETIEEKKP YEEGCLSVPD
110 120 130 140 150
IFDQVERSAR CRIRYLDYDG KQVDEWAEDL YAVCIQHEMD HLEGTLFIDY
160 170
LSRLKRDRAI DKVKKAKIRA IREDAN
Length:176
Mass (Da):20,178
Last modified:October 16, 2006 - v1
Checksum:iB7EC65796CA43467
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000158 Genomic DNA. Translation: ABI78719.1.
RefSeqiYP_759242.1. NC_008358.1.

Genome annotation databases

EnsemblBacteriaiABI78719; ABI78719; HNE_0512.
KEGGihne:HNE_0512.
PATRICi32213816. VBIHypNep17450_0513.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000158 Genomic DNA. Translation: ABI78719.1.
RefSeqiYP_759242.1. NC_008358.1.

3D structure databases

ProteinModelPortaliQ0C4V1.
SMRiQ0C4V1. Positions 2-167.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi228405.HNE_0512.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABI78719; ABI78719; HNE_0512.
KEGGihne:HNE_0512.
PATRICi32213816. VBIHypNep17450_0513.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiFDTMYEE.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciHNEP228405:GI69-512-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 15444.

Entry informationi

Entry nameiDEF_HYPNA
AccessioniPrimary (citable) accession number: Q0C4V1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 10, 2007
Last sequence update: October 16, 2006
Last modified: March 31, 2015
This is version 60 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.