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Protein

Peptide deformylase

Gene

def

Organism
Cellvibrio japonicus (strain Ueda107) (Pseudomonas fluorescens subsp. cellulosa)
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

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

Iron, Metal-binding

Enzyme and pathway databases

BioCyciCJAP498211:GHIT-3571-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:CJA_3582
OrganismiCellvibrio japonicus (strain Ueda107) (Pseudomonas fluorescens subsp. cellulosa)
Taxonomic identifieri498211 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaeCellvibrio
ProteomesiUP000001036 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 169169Peptide deformylasePRO_1000097296Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi498211.CJA_3582.

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.

B3PGY7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MALLPILEFP DPRLRTVAKP VTQVDDSIRQ LVDDMFETMY DAPGIGLAAT
60 70 80 90 100
QVNVHKRVVV IDVSEDKSQP LVFINPEIEV LDEELSQYDE GCLSVPGFYE
110 120 130 140 150
TVERPGHIRV KALDRAGNAF ELQPQGLLAV CIQHELDHLN GKLFVDHISP
160
FKRSRIRSKL EKKHKAGVR
Length:169
Mass (Da):19,064
Last modified:September 2, 2008 - v1
Checksum:i54744C6627F7CAEB
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000934 Genomic DNA. Translation: ACE82690.1.
RefSeqiWP_012489157.1. NC_010995.1.

Genome annotation databases

EnsemblBacteriaiACE82690; ACE82690; CJA_3582.
KEGGicja:CJA_3582.
PATRICi21330551. VBICelJap122165_3539.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000934 Genomic DNA. Translation: ACE82690.1.
RefSeqiWP_012489157.1. NC_010995.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi498211.CJA_3582.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACE82690; ACE82690; CJA_3582.
KEGGicja:CJA_3582.
PATRICi21330551. VBICelJap122165_3539.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiEMDQYQE.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciCJAP498211:GHIT-3571-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. "Insights into plant cell wall degradation from the genome sequence of the soil bacterium Cellvibrio japonicus."
    DeBoy R.T., Mongodin E.F., Fouts D.E., Tailford L.E., Khouri H., Emerson J.B., Mohamoud Y., Watkins K., Henrissat B., Gilbert H.J., Nelson K.E.
    J. Bacteriol. 190:5455-5463(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Ueda107.

Entry informationi

Entry nameiDEF_CELJU
AccessioniPrimary (citable) accession number: B3PGY7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: September 2, 2008
Last modified: July 22, 2015
This is version 51 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.