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Protein

Peptide deformylase

Gene

def

Organism
Rhodopseudomonas palustris (strain BisB18)
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

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

Iron, Metal-binding

Enzyme and pathway databases

BioCyciRPAL316056:GH3E-814-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:RPC_0803
OrganismiRhodopseudomonas palustris (strain BisB18)
Taxonomic identifieri316056 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBradyrhizobiaceaeRhodopseudomonas
ProteomesiUP000001948 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 175175Peptide deformylasePRO_0000301088Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi316056.RPC_0803.

Structurei

3D structure databases

ProteinModelPortaliQ21B62.
SMRiQ21B62. Positions 2-171.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiEMDQYQE.
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.

Q21B62-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MALREIIIIP DKQLRLISKP VETVSAEVRR LADDMFETMY EAPGIGLAAI
60 70 80 90 100
QVAQPVRLIT MDLVRKEGNS LTEPRAFINP EVISASEEMN VYEEGCLSIP
110 120 130 140 150
EYYAEVERPK QVRIRYTDLD GNVKEEDADG LFATCIQHEI DHLNGVLFVD
160 170
HISKLKRAMV MRKFEKAAKR GIKYV
Length:175
Mass (Da):19,922
Last modified:April 18, 2006 - v1
Checksum:i1CE28418AB10D411
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000301 Genomic DNA. Translation: ABD86374.1.
RefSeqiWP_011471282.1. NC_007925.1.

Genome annotation databases

EnsemblBacteriaiABD86374; ABD86374; RPC_0803.
KEGGirpc:RPC_0803.
PATRICi23266246. VBIRhoPal29154_0830.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000301 Genomic DNA. Translation: ABD86374.1.
RefSeqiWP_011471282.1. NC_007925.1.

3D structure databases

ProteinModelPortaliQ21B62.
SMRiQ21B62. Positions 2-171.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi316056.RPC_0803.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABD86374; ABD86374; RPC_0803.
KEGGirpc:RPC_0803.
PATRICi23266246. VBIRhoPal29154_0830.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiEMDQYQE.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciRPAL316056:GH3E-814-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: BisB18.

Entry informationi

Entry nameiDEF_RHOPB
AccessioniPrimary (citable) accession number: Q21B62
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 11, 2007
Last sequence update: April 18, 2006
Last modified: July 22, 2015
This is version 62 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.