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Protein

Peptide deformylase

Gene

def

Organism
Rhodococcus opacus (strain B4)
Status
Reviewed-Annotation score: -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)DescriptionActionsGraphical viewLength
Metal bindingi103IronUniRule annotation1
Metal bindingi145IronUniRule annotation1
Active sitei146UniRule annotation1
Metal bindingi149IronUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionHydrolase
Biological processProtein biosynthesis
LigandIron, Metal-binding

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:ROP_18920
OrganismiRhodococcus opacus (strain B4)
Taxonomic identifieri632772 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesNocardiaceaeRhodococcus
Proteomesi
  • UP000002212 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10002007431 – 196Peptide deformylaseAdd BLAST196

Interactioni

Protein-protein interaction databases

STRINGi632772.ROP_18920

Structurei

3D structure databases

SMRiC1B0D9
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4108Z02 Bacteria
COG0242 LUCA
HOGENOMiHOG000243508
KOiK01462
OMAiVCIQHEI
OrthoDBiPOG091H02B0

Family and domain databases

CDDicd00487 Pep_deformylase, 1 hit
Gene3Di3.90.45.10, 1 hit
HAMAPiMF_00163 Pep_deformylase, 1 hit
InterProiView protein in InterPro
IPR023635 Peptide_deformylase
IPR036821 Peptide_deformylase_sf
PANTHERiPTHR10458 PTHR10458, 1 hit
PfamiView protein in Pfam
PF01327 Pep_deformylase, 1 hit
PIRSFiPIRSF004749 Pep_def, 1 hit
PRINTSiPR01576 PDEFORMYLASE
SUPFAMiSSF56420 SSF56420, 1 hit
TIGRFAMsiTIGR00079 pept_deformyl, 1 hit

Sequencei

Sequence statusi: Complete.

C1B0D9-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MAILPIRIVG DPVLHEPTET VSESPAELSE LIADMYDTMD AANGVGLAAN
60 70 80 90 100
QVGIPLRLFV YDCPDVDETG KPFRRRGCVV NPVLETSERP ETMPDPDDDV
110 120 130 140 150
EGCLSVPGEQ FPTGRAEWAK VTGTDADGNA VEIEGRDFFA RMLQHEVGHL
160 170 180 190
DGFLYVDMLV GRNARAAKKT IKRAGWGVPG LSWVPGTVED PFGHDD
Length:196
Mass (Da):21,290
Last modified:May 26, 2009 - v1
Checksum:i5A16BF65861F2F64
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP011115 Genomic DNA Translation: BAH50139.1
RefSeqiWP_012689095.1, NC_012522.1

Genome annotation databases

EnsemblBacteriaiBAH50139; BAH50139; ROP_18920
KEGGirop:ROP_18920
PATRICifig|632772.20.peg.1985

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP011115 Genomic DNA Translation: BAH50139.1
RefSeqiWP_012689095.1, NC_012522.1

3D structure databases

SMRiC1B0D9
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi632772.ROP_18920

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAH50139; BAH50139; ROP_18920
KEGGirop:ROP_18920
PATRICifig|632772.20.peg.1985

Phylogenomic databases

eggNOGiENOG4108Z02 Bacteria
COG0242 LUCA
HOGENOMiHOG000243508
KOiK01462
OMAiVCIQHEI
OrthoDBiPOG091H02B0

Family and domain databases

CDDicd00487 Pep_deformylase, 1 hit
Gene3Di3.90.45.10, 1 hit
HAMAPiMF_00163 Pep_deformylase, 1 hit
InterProiView protein in InterPro
IPR023635 Peptide_deformylase
IPR036821 Peptide_deformylase_sf
PANTHERiPTHR10458 PTHR10458, 1 hit
PfamiView protein in Pfam
PF01327 Pep_deformylase, 1 hit
PIRSFiPIRSF004749 Pep_def, 1 hit
PRINTSiPR01576 PDEFORMYLASE
SUPFAMiSSF56420 SSF56420, 1 hit
TIGRFAMsiTIGR00079 pept_deformyl, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiDEF_RHOOB
AccessioniPrimary (citable) accession number: C1B0D9
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 28, 2009
Last sequence update: May 26, 2009
Last modified: September 12, 2018
This is version 55 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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