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Protein

Peptide deformylase

Gene

def

Organism
Buchnera aphidicola subsp. Acyrthosiphon pisum (strain 5A)
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

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

Iron, Metal-binding

Enzyme and pathway databases

BioCyciBAPH563178:GHDF-489-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:BUAP5A_489
OrganismiBuchnera aphidicola subsp. Acyrthosiphon pisum (strain 5A)
Taxonomic identifieri563178 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeBuchnera

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 173173Peptide deformylasePRO_1000200717Add
BLAST

Structurei

3D structure databases

ProteinModelPortaliB8D9R9.
SMRiB8D9R9. Positions 2-165.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the polypeptide deformylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiEMDQYQE.
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.

B8D9R9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSLLKILYYP DIRLRILAKP VKEINKKIQK IANDMIDTMY QEEGIGLAAT
60 70 80 90 100
QVNIPLQIIV VNTMEQKKNN LVLINPKIIK KEGDISIEEG CLSIPEYQAS
110 120 130 140 150
IPRSNYIQVQ AVNLDGEKIE IEAKSILSIC IQHEIDHLKG KLFIDYLSKF
160 170
KRERIQKKFE KINKKNKKFS IKE
Length:173
Mass (Da):20,038
Last modified:March 3, 2009 - v1
Checksum:iBAF78C26E56BED31
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001161 Genomic DNA. Translation: ACL30840.1.
RefSeqiWP_009874447.1. NC_011833.1.

Genome annotation databases

EnsemblBacteriaiACL30840; ACL30840; BUAP5A_489.
KEGGibap:BUAP5A_489.
PATRICi21243245. VBIBucAph51993_0486.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001161 Genomic DNA. Translation: ACL30840.1.
RefSeqiWP_009874447.1. NC_011833.1.

3D structure databases

ProteinModelPortaliB8D9R9.
SMRiB8D9R9. Positions 2-165.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACL30840; ACL30840; BUAP5A_489.
KEGGibap:BUAP5A_489.
PATRICi21243245. VBIBucAph51993_0486.

Phylogenomic databases

eggNOGiCOG0242.
HOGENOMiHOG000243509.
KOiK01462.
OMAiEMDQYQE.
OrthoDBiEOG664CMF.

Enzyme and pathway databases

BioCyciBAPH563178:GHDF-489-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. "The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria."
    Moran N.A., McLaughlin H.J., Sorek R.
    Science 323:379-382(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 5A.

Entry informationi

Entry nameiDEF_BUCA5
AccessioniPrimary (citable) accession number: B8D9R9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 28, 2009
Last sequence update: March 3, 2009
Last modified: July 22, 2015
This is version 47 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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.