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Protein

Peptide deformylase

Gene

def

Organism
Yersinia pestis
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

  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

BioCyciYPES214092:GKDD-238-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:YPO0242, y4023, YP_0240
OrganismiYersinia pestis
Taxonomic identifieri632 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeYersinia
ProteomesiUP000000815: Chromosome, UP000001019: Chromosome, UP000002490: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 170170Peptide deformylasePRO_0000082889Add
BLAST

Proteomic databases

PRIDEiQ8ZJ79.

Interactioni

Protein-protein interaction databases

IntActiQ8ZJ79. 4 interactions.
STRINGi214092.YPO0242.

Structurei

3D structure databases

ProteinModelPortaliQ8ZJ79.
SMRiQ8ZJ79. Positions 2-169.
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.

Q8ZJ79-1 [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:March 1, 2002 - v1
Checksum:iEB01048E0E2423A7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL590842 Genomic DNA. Translation: CAL18925.1.
AE009952 Genomic DNA. Translation: AAM87567.1.
AE017042 Genomic DNA. Translation: AAS60516.1.
PIRiAC0030.
RefSeqiNP_671316.1. NC_004088.1.
NP_991639.1. NC_005810.1.
YP_002345323.1. NC_003143.1.

Genome annotation databases

EnsemblBacteriaiAAM87567; AAM87567; y4023.
AAS60516; AAS60516; YP_0240.
GeneIDi1148970.
1173085.
2766565.
KEGGiype:YPO0242.
ypk:y4023.
ypm:YP_0240.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL590842 Genomic DNA. Translation: CAL18925.1.
AE009952 Genomic DNA. Translation: AAM87567.1.
AE017042 Genomic DNA. Translation: AAS60516.1.
PIRiAC0030.
RefSeqiNP_671316.1. NC_004088.1.
NP_991639.1. NC_005810.1.
YP_002345323.1. NC_003143.1.

3D structure databases

ProteinModelPortaliQ8ZJ79.
SMRiQ8ZJ79. Positions 2-169.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiQ8ZJ79. 4 interactions.
STRINGi214092.YPO0242.

Proteomic databases

PRIDEiQ8ZJ79.

Protocols and materials databases

DNASUi1148970.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAM87567; AAM87567; y4023.
AAS60516; AAS60516; YP_0240.
GeneIDi1148970.
1173085.
2766565.
KEGGiype:YPO0242.
ypk:y4023.
ypm:YP_0240.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiFDTMYEE.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciYPES214092:GKDD-238-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: CO-92 / Biovar Orientalis.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: KIM10+ / Biovar Mediaevalis.
  3. "Complete genome sequence of Yersinia pestis strain 91001, an isolate avirulent to humans."
    Song Y., Tong Z., Wang J., Wang L., Guo Z., Han Y., Zhang J., Pei D., Zhou D., Qin H., Pang X., Han Y., Zhai J., Li M., Cui B., Qi Z., Jin L., Dai R.
    , Chen F., Li S., Ye C., Du Z., Lin W., Wang J., Yu J., Yang H., Wang J., Huang P., Yang R.
    DNA Res. 11:179-197(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 91001 / Biovar Mediaevalis.

Entry informationi

Entry nameiDEF_YERPE
AccessioniPrimary (citable) accession number: Q8ZJ79
Secondary accession number(s): Q0WK65
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 19, 2002
Last sequence update: March 1, 2002
Last modified: January 7, 2015
This is version 91 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.