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Protein

Peptide deformylase

Gene

def

Organism
Erythrobacter litoralis (strain HTCC2594)
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 bindingi119 – 1191IronUniRule annotation
Metal bindingi161 – 1611IronUniRule annotation
Active sitei162 – 1621UniRule annotation
Metal bindingi165 – 1651IronUniRule 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

BioCyciELIT314225:GHLE-428-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:ELI_02080
OrganismiErythrobacter litoralis (strain HTCC2594)
Taxonomic identifieri314225 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaSphingomonadalesErythrobacteraceaeErythrobacter
ProteomesiUP000008808 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 194194Peptide deformylasePRO_0000301029Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi314225.ELI_02080.

Structurei

3D structure databases

ProteinModelPortaliQ2NCT3.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiGYLYIDR.
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.

Q2NCT3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAIREILEVP DPRLKTVSEP VQPDEFNDDL KQLVDDMFET MYAAPGIGLA
60 70 80 90 100
AIQVGVPKRV LVIDLQEPDM DAEPEECGHD HGDGEGAHKH YPVKNDPRIF
110 120 130 140 150
INPEIIDPNE ELSTYQEGCL SVPEIYADVD RPKTCTVKYQ DLTGKTHQED
160 170 180 190
LDGLLATCLQ HEMDHLEGIL FIDHLSRLKK QMALKKLKKM RQAA
Length:194
Mass (Da):21,910
Last modified:February 7, 2006 - v1
Checksum:i8778A6C43B8C42C3
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000157 Genomic DNA. Translation: ABC62508.1.
RefSeqiWP_011413384.1. NC_007722.1.
YP_457305.1. NC_007722.1.

Genome annotation databases

EnsemblBacteriaiABC62508; ABC62508; ELI_02080.
KEGGieli:ELI_02080.
PATRICi21857942. VBIEryLit102657_0415.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000157 Genomic DNA. Translation: ABC62508.1.
RefSeqiWP_011413384.1. NC_007722.1.
YP_457305.1. NC_007722.1.

3D structure databases

ProteinModelPortaliQ2NCT3.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi314225.ELI_02080.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABC62508; ABC62508; ELI_02080.
KEGGieli:ELI_02080.
PATRICi21857942. VBIEryLit102657_0415.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiGYLYIDR.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciELIT314225:GHLE-428-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. "Complete genome sequence of Erythrobacter litoralis HTCC2594."
    Oh H.M., Giovannoni S.J., Ferriera S., Johnson J., Cho J.C.
    J. Bacteriol. 191:2419-2420(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: HTCC2594.

Entry informationi

Entry nameiDEF_ERYLH
AccessioniPrimary (citable) accession number: Q2NCT3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 11, 2007
Last sequence update: February 7, 2006
Last modified: May 27, 2015
This is version 65 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.