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Protein

Peptide deformylase

Gene

def

Organism
Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372) (Ruminiclostridium thermocellum)
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 bindingi88 – 881IronUniRule annotation
Metal bindingi130 – 1301IronUniRule annotation
Active sitei131 – 1311UniRule annotation
Metal bindingi134 – 1341IronUniRule 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

BioCyciCTHE203119:GIW8-585-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:Cthe_0567
OrganismiClostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372) (Ruminiclostridium thermocellum)
Taxonomic identifieri203119 [NCBI]
Taxonomic lineageiBacteriaFirmicutesClostridiaClostridialesRuminococcaceaeRuminiclostridium
ProteomesiUP000002145 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 170170Peptide deformylasePRO_0000301021Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi203119.Cthe_0567.

Structurei

3D structure databases

ProteinModelPortaliA3DCX4.
SMRiA3DCX4. Positions 1-149.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiSLFVMCV.
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.

A3DCX4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAVRFIREDG DEILRKVSKK VDVIDERIKT LLDDMAETMY AANGVGLAAP
60 70 80 90 100
QVGVLKRVVV IDVGDGLMEL INPEIVEQEG EQIDIEGCLS IPGVAGEVKR
110 120 130 140 150
PARVVVEALN REGEKITVEG KELLAVALCH EIDHLDGILF TDKVIRFIDE
160 170
DEMERRRENK RRNKIRQNKG
Length:170
Mass (Da):19,085
Last modified:March 20, 2007 - v1
Checksum:i70752E03322070CD
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000568 Genomic DNA. Translation: ABN51803.1.
RefSeqiWP_003517641.1. NC_009012.1.

Genome annotation databases

EnsemblBacteriaiABN51803; ABN51803; Cthe_0567.
KEGGicth:Cthe_0567.
PATRICi19514795. VBICloThe47081_0590.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000568 Genomic DNA. Translation: ABN51803.1.
RefSeqiWP_003517641.1. NC_009012.1.

3D structure databases

ProteinModelPortaliA3DCX4.
SMRiA3DCX4. Positions 1-149.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi203119.Cthe_0567.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABN51803; ABN51803; Cthe_0567.
KEGGicth:Cthe_0567.
PATRICi19514795. VBICloThe47081_0590.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiSLFVMCV.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciCTHE203119:GIW8-585-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: ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372.

Entry informationi

Entry nameiDEF_CLOTH
AccessioniPrimary (citable) accession number: A3DCX4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 11, 2007
Last sequence update: March 20, 2007
Last modified: July 22, 2015
This is version 53 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.