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Q03F09

- DEF_PEDPA

UniProt

Q03F09 - DEF_PEDPA

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Protein

Peptide deformylase

Gene

def

Organism
Pediococcus pentosaceus (strain ATCC 25745 / 183-1w)
Status
Reviewed - 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

Binds 1 Fe2+ ion.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi111 – 1111IronUniRule annotation
Metal bindingi154 – 1541IronUniRule annotation
Active sitei155 – 1551UniRule annotation
Metal bindingi158 – 1581IronUniRule 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

BioCyciPPEN278197:GI4Y-1159-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:PEPE_1159
OrganismiPediococcus pentosaceus (strain ATCC 25745 / 183-1w)
Taxonomic identifieri278197 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesLactobacillaceaePediococcus
ProteomesiUP000000773: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 184184Peptide deformylasePRO_0000301074Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi278197.PEPE_1159.

Structurei

3D structure databases

ProteinModelPortaliQ03F09.
SMRiQ03F09. Positions 1-184.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243507.
KOiK01462.
OMAiSQDPKIA.
OrthoDBiEOG6PZXGQ.

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.

Q03F09 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MIKMNDITRD GNPVLRKRAE KLTFPLDPKY LKVADEMMEY LKNSQDPAIA
60 70 80 90 100
EKYHLRAGVG LAAPQIGLSI QMASVLVPGP DNTIDLEETL VNPVIVSQSV
110 120 130 140 150
QIAALEEGEG CLSVDKDVPG YVPRHDRITV RYQTLDGEEK TIKLRDYPAI
160 170 180
VCQHEIDHLK GTLFYDHINK ENPLDIEDNA ILIG
Length:184
Mass (Da):20,575
Last modified:November 14, 2006 - v1
Checksum:i96A9615091FAFD84
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000422 Genomic DNA. Translation: ABJ68213.1.
RefSeqiYP_804655.1. NC_008525.1.

Genome annotation databases

EnsemblBacteriaiABJ68213; ABJ68213; PEPE_1159.
GeneIDi4417622.
KEGGippe:PEPE_1159.
PATRICi22875638. VBIPedPen34213_1102.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000422 Genomic DNA. Translation: ABJ68213.1 .
RefSeqi YP_804655.1. NC_008525.1.

3D structure databases

ProteinModelPortali Q03F09.
SMRi Q03F09. Positions 1-184.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 278197.PEPE_1159.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ABJ68213 ; ABJ68213 ; PEPE_1159 .
GeneIDi 4417622.
KEGGi ppe:PEPE_1159.
PATRICi 22875638. VBIPedPen34213_1102.

Phylogenomic databases

eggNOGi COG0242.
HOGENOMi HOG000243507.
KOi K01462.
OMAi SQDPKIA.
OrthoDBi EOG6PZXGQ.

Enzyme and pathway databases

BioCyci PPEN278197:GI4Y-1159-MONOMER.

Family and domain databases

Gene3Di 3.90.45.10. 1 hit.
HAMAPi MF_00163. Pep_deformylase.
InterProi IPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view ]
PANTHERi PTHR10458. PTHR10458. 1 hit.
Pfami PF01327. Pep_deformylase. 1 hit.
[Graphical view ]
PIRSFi PIRSF004749. Pep_def. 1 hit.
PRINTSi PR01576. PDEFORMYLASE.
SUPFAMi SSF56420. SSF56420. 1 hit.
TIGRFAMsi TIGR00079. pept_deformyl. 1 hit.
ProtoNeti Search...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 25745 / 183-1w.

Entry informationi

Entry nameiDEF_PEDPA
AccessioniPrimary (citable) accession number: Q03F09
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 11, 2007
Last sequence update: November 14, 2006
Last modified: October 29, 2014
This is version 52 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