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B2K504

- DEF_YERPB

UniProt

B2K504 - DEF_YERPB

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Protein

Peptide deformylase

Gene

def

Organism
Yersinia pseudotuberculosis serotype IB (strain PB1/+)
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 bindingi91 – 911IronUniRule annotation
Metal bindingi133 – 1331IronUniRule annotation
Active sitei134 – 1341UniRule annotation
Metal bindingi137 – 1371IronUniRule 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

BioCyciYPSE502801:GHIH-3998-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:YPTS_3857
OrganismiYersinia pseudotuberculosis serotype IB (strain PB1/+)
Taxonomic identifieri502801 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeYersinia
ProteomesiUP000001193: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 170170Peptide deformylasePRO_1000097363Add
BLAST

Proteomic databases

PRIDEiB2K504.

Interactioni

Protein-protein interaction databases

STRINGi502801.YPTS_3857.

Structurei

3D structure databases

ProteinModelPortaliB2K504.
SMRiB2K504. Positions 2-169.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiELLAICI.
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.

B2K504-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSVLQVLHYP DERLRKIAAP VKEVNGEIQR IVDDMFETMY AEEGIGLAAT
60 70 80 90 100
QVDVHQQIIV IDISENRDQR LVLINPELLE KSGETGIEEG CLSIPEQRAL
110 120 130 140 150
VPRAEKVKIR ALDRDGKPFE LETDGLLAIC IQHEMDHLIG KLFVDYLSPL
160 170
KRQRIRQKLE KMAKLNARAN
Length:170
Mass (Da):19,391
Last modified:June 10, 2008 - v1
Checksum:iEB01048E0E2423A7
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP001048 Genomic DNA. Translation: ACC90806.1.
RefSeqiYP_001874263.1. NC_010634.1.

Genome annotation databases

EnsemblBacteriaiACC90806; ACC90806; YPTS_3857.
GeneIDi6260484.
KEGGiypb:YPTS_3857.
PATRICi18655996. VBIYerPse20639_4179.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP001048 Genomic DNA. Translation: ACC90806.1 .
RefSeqi YP_001874263.1. NC_010634.1.

3D structure databases

ProteinModelPortali B2K504.
SMRi B2K504. Positions 2-169.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 502801.YPTS_3857.

Proteomic databases

PRIDEi B2K504.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ACC90806 ; ACC90806 ; YPTS_3857 .
GeneIDi 6260484.
KEGGi ypb:YPTS_3857.
PATRICi 18655996. VBIYerPse20639_4179.

Phylogenomic databases

eggNOGi COG0242.
HOGENOMi HOG000243509.
KOi K01462.
OMAi ELLAICI.
OrthoDBi EOG664CMF.

Enzyme and pathway databases

BioCyci YPSE502801:GHIH-3998-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. "Complete sequence of Yersinia pseudotuberculosis PB1/+."
    Copeland A., Lucas S., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., Munk A.C., Brettin T., Detter J.C., Han C., Tapia R., Schmutz J., Larimer F., Land M., Hauser L.
    , Challacombe J.F., Green L., Lindler L.E., Nikolich M.P., Richardson P.
    Submitted (APR-2008) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: PB1/+.

Entry informationi

Entry nameiDEF_YERPB
AccessioniPrimary (citable) accession number: B2K504
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: June 10, 2008
Last modified: October 1, 2014
This is version 40 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