Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Peptide deformylase

Gene

def

Organism
Pelodictyon phaeoclathratiforme (strain DSM 5477 / BU-1)
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

BioCyciPPHA324925:GHBF-1821-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:Ppha_1788
OrganismiPelodictyon phaeoclathratiforme (strain DSM 5477 / BU-1)
Taxonomic identifieri324925 [NCBI]
Taxonomic lineageiBacteriaChlorobiChlorobiaChlorobialesChlorobiaceaeChlorobium/Pelodictyon groupPelodictyon
ProteomesiUP000002724 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 188188Peptide deformylasePRO_1000097330Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi324925.Ppha_1788.

Structurei

3D structure databases

ProteinModelPortaliB4SBG6.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiDTMLEMD.
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.

B4SBG6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MILPINIYSD DILRLKAKPL KGVDSAIEEL IASMFESMRN ASGIGLAAPQ
60 70 80 90 100
VGRSIRLLVL DVSCVSKCEH EKPMVVINPH ILSVRGHNDM EEGCLSVPGV
110 120 130 140 150
QGYVVRPAAI TLKYRDEHFA ERTGEFSGMV ARVIQHEIDH LDGTLFVDRM
160 170 180
EKRDRKKIQK ELTALASGIV DTEYPVVERE VVPIAKPT
Length:188
Mass (Da):20,886
Last modified:September 23, 2008 - v1
Checksum:i7794A6B171AC4E52
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001110 Genomic DNA. Translation: ACF44020.1.
RefSeqiWP_012508507.1. NC_011060.1.
YP_002018637.1. NC_011060.1.

Genome annotation databases

EnsemblBacteriaiACF44020; ACF44020; Ppha_1788.
KEGGipph:Ppha_1788.
PATRICi22904278. VBIPelPha134556_1918.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001110 Genomic DNA. Translation: ACF44020.1.
RefSeqiWP_012508507.1. NC_011060.1.
YP_002018637.1. NC_011060.1.

3D structure databases

ProteinModelPortaliB4SBG6.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi324925.Ppha_1788.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACF44020; ACF44020; Ppha_1788.
KEGGipph:Ppha_1788.
PATRICi22904278. VBIPelPha134556_1918.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiDTMLEMD.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciPPHA324925:GHBF-1821-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. "Complete sequence of Pelodictyon phaeoclathratiforme BU-1."
    US DOE Joint Genome Institute
    Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N., Liu Z., Li T., Zhao F.
    , Overmann J., Bryant D.A., Richardson P.
    Submitted (JUN-2008) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: DSM 5477 / BU-1.

Entry informationi

Entry nameiDEF_PELPB
AccessioniPrimary (citable) accession number: B4SBG6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: September 23, 2008
Last modified: May 27, 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, 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.