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Protein

Peptide deformylase

Gene

def

Organism
Oligotropha carboxidovorans (strain ATCC 49405 / DSM 1227 / OM5)
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 bindingi94 – 941IronUniRule annotation
Metal bindingi136 – 1361IronUniRule annotation
Active sitei137 – 1371UniRule annotation
Metal bindingi140 – 1401IronUniRule 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

BioCyciOCAR504832:GJPZ-600-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:OCAR_7540, OCA5_c06000
OrganismiOligotropha carboxidovorans (strain ATCC 49405 / DSM 1227 / OM5)
Taxonomic identifieri504832 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBradyrhizobiaceaeOligotropha
ProteomesiUP000001678: Chromosome, UP000007730: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 171171Peptide deformylasePRO_1000097327Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi504832.OCAR_7540.

Structurei

3D structure databases

ProteinModelPortaliB6JJP8.
SMRiB6JJP8. Positions 2-170.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiFDTMYEE.
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.

B6JJP8-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MAIREIISIP DKRLRRVSEP VEKITSEVRA LAEDMFETMY DAPGIGLAAI
60 70 80 90 100
QVAVPLRLIT MDLAKKEGES APRVFINPEI LSKSEDIAVY EEGCLSIPEY
110 120 130 140 150
YEEVERPASV RVRFMDLEGE VHEEDAEGLF ATCIQHEIDH LNGVLFIDYL
160 170
SKLKRDRVMK KFTKAAKLAA K
Length:171
Mass (Da):19,367
Last modified:December 16, 2008 - v1
Checksum:iEB0D04A8BF41330E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001196 Genomic DNA. Translation: ACI94642.1.
CP002826 Genomic DNA. Translation: AEI05324.1.
RefSeqiYP_002290507.1. NC_011386.1.
YP_004631565.1. NC_015684.1.

Genome annotation databases

EnsemblBacteriaiACI94642; ACI94642; OCAR_7540.
AEI05324; AEI05324; OCA5_c06000.
GeneIDi10845732.
6990043.
KEGGioca:OCAR_7540.
ocg:OCA5_c06000.
PATRICi22808857. VBIOliCar134280_3371.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001196 Genomic DNA. Translation: ACI94642.1.
CP002826 Genomic DNA. Translation: AEI05324.1.
RefSeqiYP_002290507.1. NC_011386.1.
YP_004631565.1. NC_015684.1.

3D structure databases

ProteinModelPortaliB6JJP8.
SMRiB6JJP8. Positions 2-170.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi504832.OCAR_7540.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACI94642; ACI94642; OCAR_7540.
AEI05324; AEI05324; OCA5_c06000.
GeneIDi10845732.
6990043.
KEGGioca:OCAR_7540.
ocg:OCA5_c06000.
PATRICi22808857. VBIOliCar134280_3371.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiFDTMYEE.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciOCAR504832:GJPZ-600-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. "Genome sequence of the chemolithoautotrophic bacterium Oligotropha carboxidovorans OM5T."
    Paul D., Bridges S., Burgess S.C., Dandass Y., Lawrence M.L.
    J. Bacteriol. 190:5531-5532(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 49405 / DSM 1227 / OM5.
  2. "Complete genome sequences of the chemolithoautotrophic Oligotropha carboxidovorans strains OM4 and OM5."
    Volland S., Rachinger M., Strittmatter A., Daniel R., Gottschalk G., Meyer O.
    J. Bacteriol. 193:5043-5043(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 49405 / DSM 1227 / OM5.

Entry informationi

Entry nameiDEF_OLICO
AccessioniPrimary (citable) accession number: B6JJP8
Secondary accession number(s): F8BWX2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: December 16, 2008
Last modified: January 7, 2015
This is version 39 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.