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Protein

Peptide deformylase

Gene

def

Organism
Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672) (Erwinia carotovora subsp. atroseptica)
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

BioCyciPATR218491:GJNB-4082-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:ECA3999
OrganismiPectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672) (Erwinia carotovora subsp. atroseptica)
Taxonomic identifieri218491 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaePectobacterium
ProteomesiUP000007966 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 169169Peptide deformylasePRO_0000301028Add
BLAST

Proteomic databases

PRIDEiQ6D002.

Interactioni

Protein-protein interaction databases

STRINGi218491.ECA3999.

Structurei

3D structure databases

ProteinModelPortaliQ6D002.
SMRiQ6D002. 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.

Q6D002-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSVLQVLHFP DERLRITAQP VKEVNADIQR IVDDMFDTMY EEEGIGLAAT
60 70 80 90 100
QVDIHQRIIV IDVSEERDQR LVLINPELIE KSGDTGIEEG CLSIPETRAL
110 120 130 140 150
VPRAEHVKVR ALDREGKAFE LEASELLAIC IQHEMDHLVG KLFIDYLSPL
160
KRQRIRQKLE KLAKQNSRT
Length:169
Mass (Da):19,377
Last modified:August 16, 2004 - v1
Checksum:i16C8E821C0012D60
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BX950851 Genomic DNA. Translation: CAG76896.1.
RefSeqiWP_011095493.1. NC_004547.2.
YP_052086.1. NC_004547.2.

Genome annotation databases

EnsemblBacteriaiCAG76896; CAG76896; ECA3999.
GeneIDi2881920.
KEGGieca:ECA3999.
PATRICi20483439. VBIPecAtr54885_4065.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BX950851 Genomic DNA. Translation: CAG76896.1.
RefSeqiWP_011095493.1. NC_004547.2.
YP_052086.1. NC_004547.2.

3D structure databases

ProteinModelPortaliQ6D002.
SMRiQ6D002. Positions 2-168.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi218491.ECA3999.

Proteomic databases

PRIDEiQ6D002.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAG76896; CAG76896; ECA3999.
GeneIDi2881920.
KEGGieca:ECA3999.
PATRICi20483439. VBIPecAtr54885_4065.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiFDTMYEE.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciPATR218491:GJNB-4082-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: SCRI 1043 / ATCC BAA-672.

Entry informationi

Entry nameiDEF_PECAS
AccessioniPrimary (citable) accession number: Q6D002
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 11, 2007
Last sequence update: August 16, 2004
Last modified: April 1, 2015
This is version 68 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.