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Protein

Peptide deformylase

Gene

def

Organism
Pelagibacter ubique (strain HTCC1062)
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 bindingi94 – 941IronUniRule annotation
Metal bindingi136 – 1361IronUniRule annotation
Active sitei137 – 1371UniRule annotation
Metal bindingi140 – 1401IronUniRule 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

BioCyciCPEL335992:GH3Z-460-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:SAR11_0456
OrganismiPelagibacter ubique (strain HTCC1062)
Taxonomic identifieri335992 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaPelagibacteralesPelagibacteraceaeCandidatus Pelagibacter
ProteomesiUP000002528 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 172172Peptide deformylasePRO_0000301075Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi335992.SAR11_0456.

Structurei

3D structure databases

ProteinModelPortaliQ4FNG1.
SMRiQ4FNG1. Positions 2-168.
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.

Q4FNG1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSVKSILTEP NKLLRQISKP VENVGDEERR LMDDMLDTMY AAPGIGLAAI
60 70 80 90 100
QIGVPKRIIV MDISRDEDKK EPRYFVNPVI KNKNDITSKY EEGCLSVPDQ
110 120 130 140 150
FAEIERPNEC EVEYLDYNGK KQLLKADGLL ATCIQHEMDH LEGVLFIDYL
160 170
SKLKKSMIIK KLSKIKSNRI IV
Length:172
Mass (Da):19,669
Last modified:August 30, 2005 - v1
Checksum:i3EC788BF93124669
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000084 Genomic DNA. Translation: AAZ21278.1.
RefSeqiWP_011281724.1. NC_007205.1.

Genome annotation databases

EnsemblBacteriaiAAZ21278; AAZ21278; SAR11_0456.
KEGGipub:SAR11_0456.
PATRICi31990377. VBICanPel5618_0455.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000084 Genomic DNA. Translation: AAZ21278.1.
RefSeqiWP_011281724.1. NC_007205.1.

3D structure databases

ProteinModelPortaliQ4FNG1.
SMRiQ4FNG1. Positions 2-168.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi335992.SAR11_0456.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAZ21278; AAZ21278; SAR11_0456.
KEGGipub:SAR11_0456.
PATRICi31990377. VBICanPel5618_0455.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiEMDQYQE.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciCPEL335992:GH3Z-460-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: HTCC1062.

Entry informationi

Entry nameiDEF_PELUB
AccessioniPrimary (citable) accession number: Q4FNG1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 11, 2007
Last sequence update: August 30, 2005
Last modified: July 22, 2015
This is version 67 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.