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Protein

Peptide deformylase

Gene

def

Organism
Prochlorococcus marinus (strain MIT 9515)
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 bindingi121 – 1211IronUniRule annotation
Metal bindingi163 – 1631IronUniRule annotation
Active sitei164 – 1641UniRule annotation
Metal bindingi167 – 1671IronUniRule 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

BioCyciPMAR167542:GI3N-79-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:P9515_00771
OrganismiProchlorococcus marinus (strain MIT 9515)
Taxonomic identifieri167542 [NCBI]
Taxonomic lineageiBacteriaCyanobacteriaProchloralesProchlorococcaceaeProchlorococcus
ProteomesiUP000001589: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 203203Peptide deformylasePRO_0000301079Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi167542.P9515_00771.

Structurei

3D structure databases

ProteinModelPortaliA2BU25.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiRENKMAR.
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.

A2BU25-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MANNFSQLAK KSRNELSSSK VKKEVIENPP LEIFKLGNDV LRTNAKRIGK
60 70 80 90 100
VDLDTRNLAK DMLKSMYSAK GIGLAAPQVG ISKELLVIDI NFEDSAAEPL
110 120 130 140 150
ILINPEITAF GNTLNSYEEG CLSIPGVYLN VVRPSTIKLR FSDEMGRPRK
160 170 180 190 200
MNADGLLARC IQHEVDHLRG VLFVDRVTSK EDLKTELKKE GFQMKDVFPI

SQS
Length:203
Mass (Da):22,635
Last modified:February 20, 2007 - v1
Checksum:i240789A1AE32E960
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000552 Genomic DNA. Translation: ABM71286.1.
RefSeqiWP_011819403.1. NC_008817.1.
YP_001010393.1. NC_008817.1.

Genome annotation databases

EnsemblBacteriaiABM71286; ABM71286; P9515_00771.
GeneIDi4719954.
KEGGipmc:P9515_00771.
PATRICi23013668. VBIProMar113831_0078.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000552 Genomic DNA. Translation: ABM71286.1.
RefSeqiWP_011819403.1. NC_008817.1.
YP_001010393.1. NC_008817.1.

3D structure databases

ProteinModelPortaliA2BU25.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi167542.P9515_00771.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABM71286; ABM71286; P9515_00771.
GeneIDi4719954.
KEGGipmc:P9515_00771.
PATRICi23013668. VBIProMar113831_0078.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiRENKMAR.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciPMAR167542:GI3N-79-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: MIT 9515.

Entry informationi

Entry nameiDEF_PROM5
AccessioniPrimary (citable) accession number: A2BU25
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 11, 2007
Last sequence update: February 20, 2007
Last modified: February 4, 2015
This is version 48 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

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.