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Protein

Peptide deformylase

Gene

def

Organism
Polynucleobacter necessarius subsp. necessarius (strain STIR1)
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 bindingi92 – 921IronUniRule annotation
Metal bindingi134 – 1341IronUniRule annotation
Active sitei135 – 1351UniRule annotation
Metal bindingi138 – 1381IronUniRule 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

BioCyciPNEC452638:GI4T-1774-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:Pnec_1778
OrganismiPolynucleobacter necessarius subsp. necessarius (strain STIR1)
Taxonomic identifieri452638 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesBurkholderiaceaePolynucleobacter
ProteomesiUP000006582: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 171171Peptide deformylasePRO_1000097332Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi452638.Pnec_1778.

Structurei

3D structure databases

ProteinModelPortaliB1XSN2.
SMRiB1XSN2. Positions 2-166.
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.

B1XSN2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MALLTVLCYP DSRLHKVAKP VAQVDARIKK IVADMADTMY EAPGVGLAAT
60 70 80 90 100
QVDIHERIVV IDVSDEQNEL MVFINPEIVW TSSETKSWRE GCLSVPEFYD
110 120 130 140 150
EVERPAEIRV KALDIDGKEF EIEADGSLAV CLQHELDHLQ GKVFVEYLSI
160 170
FKRTRISQKM KKRAKELIGQ R
Length:171
Mass (Da):19,429
Last modified:May 20, 2008 - v1
Checksum:i08FE68FC24DF4974
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001010 Genomic DNA. Translation: ACB44831.1.
RefSeqiYP_001798445.1. NC_010531.1.

Genome annotation databases

EnsemblBacteriaiACB44831; ACB44831; Pnec_1778.
GeneIDi6184595.
KEGGipne:Pnec_1778.
PATRICi22972894. VBIPolNec8289_2040.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001010 Genomic DNA. Translation: ACB44831.1.
RefSeqiYP_001798445.1. NC_010531.1.

3D structure databases

ProteinModelPortaliB1XSN2.
SMRiB1XSN2. Positions 2-166.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi452638.Pnec_1778.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACB44831; ACB44831; Pnec_1778.
GeneIDi6184595.
KEGGipne:Pnec_1778.
PATRICi22972894. VBIPolNec8289_2040.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiFDTMYEE.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciPNEC452638:GI4T-1774-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: STIR1.

Entry informationi

Entry nameiDEF_POLNS
AccessioniPrimary (citable) accession number: B1XSN2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: May 20, 2008
Last modified: January 7, 2015
This is version 42 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.