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Protein

Peptide deformylase

Gene

def

Organism
Tropheryma whipplei (strain Twist) (Whipple's bacillus)
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 bindingi141 – 1411IronUniRule annotation
Metal bindingi183 – 1831IronUniRule annotation
Active sitei184 – 1841UniRule annotation
Metal bindingi187 – 1871IronUniRule 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

BioCyciTWHI203267:GJDK-331-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:TWT_310
OrganismiTropheryma whipplei (strain Twist) (Whipple's bacillus)
Taxonomic identifieri203267 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesMicrococcineaeTropheryma
ProteomesiUP000002200 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 228228Peptide deformylasePRO_0000082871Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi203267.TWT310.

Structurei

3D structure databases

ProteinModelPortaliQ83GH8.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
KOiK01462.
OMAiDTMLEMD.
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.

Q83GH8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSQDRRYTGC NTHSNTHSAQ DREKEGAVPK ISGGKILPIY ITGHAVLHAP
60 70 80 90 100
AKPVTDFSGI QEIVRDMFAT MFAAPGVGLA GPQIGLGLRI FVYSYTEGDT
110 120 130 140 150
LHQGVAINPD LLIPKGVPKR QTNKQQANNS TSCDEPDREG CLSFPGYQFP
160 170 180 190 200
LERAPQVTLS AFDENKKPFT VHATGWLARI FQHEFDHLQG TLYVDRLAQK
210 220
YSGEVRQAVL NNKWGIPGKY WVPQEPKE
Length:228
Mass (Da):25,290
Last modified:June 1, 2003 - v1
Checksum:iA02523288B7E07C6
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE014184 Genomic DNA. Translation: AAO44407.1.
RefSeqiNP_787438.1. NC_004572.3.
WP_011102496.1. NC_004572.3.

Genome annotation databases

EnsemblBacteriaiAAO44407; AAO44407; TWT_310.
KEGGitwh:TWT310.
PATRICi23997121. VBITroWhi72342_0440.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE014184 Genomic DNA. Translation: AAO44407.1.
RefSeqiNP_787438.1. NC_004572.3.
WP_011102496.1. NC_004572.3.

3D structure databases

ProteinModelPortaliQ83GH8.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi203267.TWT310.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAO44407; AAO44407; TWT_310.
KEGGitwh:TWT310.
PATRICi23997121. VBITroWhi72342_0440.

Phylogenomic databases

eggNOGiCOG0242.
KOiK01462.
OMAiDTMLEMD.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciTWHI203267:GJDK-331-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. "Tropheryma whipplei twist: a human pathogenic Actinobacteria with a reduced genome."
    Raoult D., Ogata H., Audic S., Robert C., Suhre K., Drancourt M., Claverie J.-M.
    Genome Res. 13:1800-1809(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Twist.

Entry informationi

Entry nameiDEF_TROWT
AccessioniPrimary (citable) accession number: Q83GH8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 2003
Last sequence update: June 1, 2003
Last modified: April 29, 2015
This is version 81 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.