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Protein

Peptide deformylase

Gene

def

Organism
Haemophilus ducreyi (strain 35000HP / ATCC 700724)
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

BioCyciHDUC233412:GH5F-1702-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:HD_1889
OrganismiHaemophilus ducreyi (strain 35000HP / ATCC 700724)
Taxonomic identifieri233412 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPasteurellalesPasteurellaceaeHaemophilus
ProteomesiUP000001022 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 171171Peptide deformylasePRO_0000082787Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi233412.HD1889.

Structurei

3D structure databases

ProteinModelPortaliQ7VKK9.
SMRiQ7VKK9. Positions 2-168.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
KOiK01462.
OMAiEMDQYQE.
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.

Q7VKK9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSVLQVVLYP DDRLTKVCEP VTQVDDELNQ FIDDMFDTMY QEGGIGLAAS
60 70 80 90 100
QVGVLKRVIT IDIEGDKTNQ VVLINPEILE SCGETGIEEG CLSIPGYRAL
110 120 130 140 150
VPRKEKITVK ALNRQGEEVI YHADDLFAIC IQHEIDHLNG IVFVDHISNL
160 170
KRQRIKDKMQ KLKKQLYRSK A
Length:171
Mass (Da):19,369
Last modified:October 1, 2003 - v1
Checksum:i344DCD9AB278CC12
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE017143 Genomic DNA. Translation: AAP96618.1.
RefSeqiWP_010945646.1. NC_002940.2.

Genome annotation databases

EnsemblBacteriaiAAP96618; AAP96618; HD_1889.
KEGGihdu:HD1889.
PATRICi20179926. VBIHaeDuc133973_1583.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE017143 Genomic DNA. Translation: AAP96618.1.
RefSeqiWP_010945646.1. NC_002940.2.

3D structure databases

ProteinModelPortaliQ7VKK9.
SMRiQ7VKK9. Positions 2-168.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi233412.HD1889.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAP96618; AAP96618; HD_1889.
KEGGihdu:HD1889.
PATRICi20179926. VBIHaeDuc133973_1583.

Phylogenomic databases

eggNOGiCOG0242.
KOiK01462.
OMAiEMDQYQE.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciHDUC233412:GH5F-1702-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. "The complete genome sequence of Haemophilus ducreyi."
    Munson R.S. Jr., Ray W.C., Mahairas G., Sabo P., Mungur R., Johnson L., Nguyen D., Wang J., Forst C., Hood L.
    Submitted (JUN-2003) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 35000HP / ATCC 700724.

Entry informationi

Entry nameiDEF_HAEDU
AccessioniPrimary (citable) accession number: Q7VKK9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 2003
Last sequence update: October 1, 2003
Last modified: July 22, 2015
This is version 74 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.