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Protein

Peptide deformylase

Gene

def

Organism
Vibrio campbellii (strain ATCC BAA-1116 / BB120)
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 bindingi91 – 911IronUniRule annotation
Metal bindingi133 – 1331IronUniRule annotation
Active sitei134 – 1341UniRule annotation
Metal bindingi137 – 1371IronUniRule 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

BioCyciVHAR338187:GJCH-384-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:VIBHAR_00391
OrganismiVibrio campbellii (strain ATCC BAA-1116 / BB120)
Taxonomic identifieri338187 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
ProteomesiUP000008152 Componenti: Chromosome I

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 172172Peptide deformylasePRO_1000023138Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi338187.VIBHAR_00391.

Structurei

3D structure databases

ProteinModelPortaliA7N121.
SMRiA7N121. Positions 2-168.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiFDTMYEE.
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.

A7N121-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSVLQVLTFP DDRLRTVAKP VEEVTPEIQK IVDDMIETMY DEEGIGLAAT
60 70 80 90 100
QVDIHKRIVV IDISETRDEP MVLINPEILE KRGEDGIEEG CLSVPGARAL
110 120 130 140 150
VPRAAEVTVK ALDRDGKEYT FEADDLLAIC VQHELDHLMG KLFVDYLSPL
160 170
KRKRIQDKLA KIKRFNEKQQ NA
Length:172
Mass (Da):19,496
Last modified:October 2, 2007 - v1
Checksum:i9EBF4AC4001AA919
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000789 Genomic DNA. Translation: ABU69406.1.
RefSeqiWP_005450979.1. NC_022269.1.
YP_008526900.1. NC_022269.1.

Genome annotation databases

EnsemblBacteriaiABU69406; ABU69406; VIBHAR_00391.
KEGGivca:M892_10785.
vha:VIBHAR_00391.
PATRICi20127663. VBIVibHar24526_0414.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000789 Genomic DNA. Translation: ABU69406.1.
RefSeqiWP_005450979.1. NC_022269.1.
YP_008526900.1. NC_022269.1.

3D structure databases

ProteinModelPortaliA7N121.
SMRiA7N121. Positions 2-168.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi338187.VIBHAR_00391.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABU69406; ABU69406; VIBHAR_00391.
KEGGivca:M892_10785.
vha:VIBHAR_00391.
PATRICi20127663. VBIVibHar24526_0414.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiFDTMYEE.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciVHAR338187:GJCH-384-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: ATCC BAA-1116 / BB120.

Entry informationi

Entry nameiDEF_VIBCB
AccessioniPrimary (citable) accession number: A7N121
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: October 2, 2007
Last modified: May 27, 2015
This is version 47 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.