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Protein

Peptide deformylase

Gene

def

Organism
Desulforudis audaxviator (strain MP104C)
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 bindingi90 – 901IronUniRule annotation
Metal bindingi132 – 1321IronUniRule annotation
Active sitei133 – 1331UniRule annotation
Metal bindingi136 – 1361IronUniRule 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

BioCyciDAUD477974:GH0B-1637-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:Daud_1593
OrganismiDesulforudis audaxviator (strain MP104C)
Taxonomic identifieri477974 [NCBI]
Taxonomic lineageiBacteriaFirmicutesClostridiaClostridialesPeptococcaceaeCandidatus Desulforudis
ProteomesiUP000008544 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 154154Peptide deformylasePRO_1000097303Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi477974.Daud_1593.

Structurei

3D structure databases

ProteinModelPortaliB1I504.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243508.
KOiK01462.
OMAiIRSAEWY.
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.

B1I504-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAVFQIVQYP DPILREKARE VRKITPQIER LAVNLVDTMR RSGGVGLAAP
60 70 80 90 100
QIGVSKRVIV VEDPEKNPIV LINPEIVRLE GDKETAEEGC LSVPGVWGQV
110 120 130 140 150
ERRMCLTVRG YNLEGKQVAY LVEGFTARAF QHEIDHLDGI VFLDRATTIY

KRKE
Length:154
Mass (Da):17,368
Last modified:April 29, 2008 - v1
Checksum:i227066B281A0A6A8
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000860 Genomic DNA. Translation: ACA60095.1.
RefSeqiWP_012302676.1. NC_010424.1.
YP_001717727.1. NC_010424.1.

Genome annotation databases

EnsemblBacteriaiACA60095; ACA60095; Daud_1593.
KEGGidau:Daud_1593.
PATRICi31970056. VBICanDes92303_1650.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000860 Genomic DNA. Translation: ACA60095.1.
RefSeqiWP_012302676.1. NC_010424.1.
YP_001717727.1. NC_010424.1.

3D structure databases

ProteinModelPortaliB1I504.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi477974.Daud_1593.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACA60095; ACA60095; Daud_1593.
KEGGidau:Daud_1593.
PATRICi31970056. VBICanDes92303_1650.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243508.
KOiK01462.
OMAiIRSAEWY.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciDAUD477974:GH0B-1637-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 chromosome of Desulforudis audaxviator MP104C."
    Copeland A., Lucas S., Lapidus A., Barry K., Glavina del Rio T., Dalin E., Tice H., Bruce D., Pitluck S., Lowry S.R., Larimer F., Land M.L., Hauser L., Kyrpides N., Ivanova N.N., Richardson P.
    Submitted (OCT-2007) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: MP104C.

Entry informationi

Entry nameiDEF_DESAP
AccessioniPrimary (citable) accession number: B1I504
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: April 29, 2008
Last modified: May 27, 2015
This is version 50 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.