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Protein

Peptide deformylase

Gene

def

Organism
Symbiobacterium thermophilum (strain T / IAM 14863)
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

BioCyciSTHE292459:GJMM-1412-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:STH1343
OrganismiSymbiobacterium thermophilum (strain T / IAM 14863)
Taxonomic identifieri292459 [NCBI]
Taxonomic lineageiBacteriaFirmicutesClostridiaClostridialesSymbiobacteriaceaeSymbiobacterium
ProteomesiUP000000417 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 217217Peptide deformylasePRO_0000301114Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi292459.STH1343.

Structurei

3D structure databases

ProteinModelPortaliQ67PR5.
SMRiQ67PR5. Positions 1-149.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243508.
KOiK01462.
OMAiAEWHELE.
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]
PRINTSiPR01576. PDEFORMYLASE.
SUPFAMiSSF56420. SSF56420. 1 hit.
TIGRFAMsiTIGR00079. pept_deformyl. 1 hit.

Sequencei

Sequence statusi: Complete.

Q67PR5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAILEIVKEP AEVLRKKAKP VTKINASIRK LLDDMTETMY AAPGVGLAAP
60 70 80 90 100
QVGVSKRLIV VDPQDGSGQL YQLINPEIVK AEGWVKGTEG CLSIPGMVGD
110 120 130 140 150
VWRYEKVQVV ALDRTGKKVW IDAEGYLARI FQHEIDHLDG ILYTDKCTNL
160 170 180 190 200
RPVSEDGEEE EEAEVAEVMP EPEAEGAGEP SAEGAGQAAA EAGAEEGEQV
210
TTGVSGERRG SAAAKEE
Length:217
Mass (Da):23,242
Last modified:October 10, 2004 - v1
Checksum:iDAA0BEF5C915026C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP006840 Genomic DNA. Translation: BAD40328.1.
RefSeqiYP_075172.1. NC_006177.1.

Genome annotation databases

EnsemblBacteriaiBAD40328; BAD40328; STH1343.
GeneIDi2979184.
KEGGisth:STH1343.
PATRICi23780837. VBISymThe116959_1339.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP006840 Genomic DNA. Translation: BAD40328.1.
RefSeqiYP_075172.1. NC_006177.1.

3D structure databases

ProteinModelPortaliQ67PR5.
SMRiQ67PR5. Positions 1-149.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi292459.STH1343.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAD40328; BAD40328; STH1343.
GeneIDi2979184.
KEGGisth:STH1343.
PATRICi23780837. VBISymThe116959_1339.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243508.
KOiK01462.
OMAiAEWHELE.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciSTHE292459:GJMM-1412-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]
PRINTSiPR01576. PDEFORMYLASE.
SUPFAMiSSF56420. SSF56420. 1 hit.
TIGRFAMsiTIGR00079. pept_deformyl. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "Genome sequence of Symbiobacterium thermophilum, an uncultivable bacterium that depends on microbial commensalism."
    Ueda K., Yamashita A., Ishikawa J., Shimada M., Watsuji T., Morimura K., Ikeda H., Hattori M., Beppu T.
    Nucleic Acids Res. 32:4937-4944(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: T / IAM 14863.

Entry informationi

Entry nameiDEF_SYMTH
AccessioniPrimary (citable) accession number: Q67PR5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 10, 2007
Last sequence update: October 10, 2004
Last modified: March 31, 2015
This is version 70 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.