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B4RDT8 (DEF_PHEZH) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 26. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (1) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
Peptide deformylase
Short name=PDF
EC=3.5.1.88
Alternative name(s):
Polypeptide deformylase
Gene names
Name:def
Ordered Locus Names:PHZ_c0373
OrganismPhenylobacterium zucineum (strain HLK1) [Complete proteome] [HAMAP]
Taxonomic identifier450851 [NCBI]
Taxonomic lineageBacteria › Proteobacteria › Alphaproteobacteria › Caulobacterales › Caulobacteraceae › Phenylobacterium

Protein attributes

Sequence length169 AA.
Sequence statusComplete.
Protein existenceInferred from homology

General annotation (Comments)

Function

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 By similarity. HAMAP MF_00163

Catalytic activity

Formyl-L-methionyl peptide + H2O = formate + methionyl peptide. HAMAP MF_00163

Cofactor

Binds 1 Fe2+ ion By similarity. HAMAP MF_00163

Sequence similarities

Belongs to the polypeptide deformylase family.

Ontologies

Keywords
   Biological processProtein biosynthesis
   LigandIron
Metal-binding
   Molecular functionHydrolase
   Technical termComplete proteome
Gene Ontology (GO)
   Biological processtranslation

Inferred from electronic annotation. Source: UniProtKB-KW

   Molecular functioniron ion binding

Inferred from electronic annotation. Source: InterPro

peptide deformylase activity

Inferred from electronic annotation. Source: EC

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 169169Peptide deformylase HAMAP MF_00163
PRO_1000097331

Sites

Active site1371 By similarity
Metal binding941Iron By similarity
Metal binding1361Iron By similarity
Metal binding1401Iron By similarity

Sequences

Sequence LengthMass (Da)Tools
B4RDT8 [UniParc].

Last modified September 23, 2008. Version 1.
Checksum: 1A32B4B2E9EE7FAD

FASTA16919,255
        10         20         30         40         50         60 
MAIREILVVP HPALKQVSQP VEKVDDELRA LMDDMLETMY AAPGIGLAAI QIGVPKRVIV 

        70         80         90        100        110        120 
MDLAREGEEK QPRYFVNPEI LWASDDTAPY EEGCLSVPEY YDEVERPARV KLRYLNYQGE 

       130        140        150        160 
QVEEDAEGLF AVCIQHEMDH LEGVLFIDHL SRLKREQAIK KVKKHAKAA

« Hide

References

[1]"Complete genome of Phenylobacterium zucineum - a novel facultative intracellular bacterium isolated from human erythroleukemia cell line K562."
Luo Y., Xu X., Ding Z., Liu Z., Zhang B., Yan Z., Sun J., Hu S., Hu X.
BMC Genomics 9:386-386(2008) [PubMed: 18700039] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: HLK1.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		CP000747 Genomic DNA. Translation: ACG76787.1.
RefSeqYP_002129216.1. NC_011144.1.

3D structure databases

ModBaseSearch...

Protein-protein interaction databases

STRINGB4RDT8.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID6789863.
GenomeReviewsGene locus PHZ_c0373 in contig CP000747_GR.
KEGGpzu:PHZ_c0373.
PATRIC22923332. VBIPheZuc44517_0761.

Organism-specific databases

CMRSearch...

Phylogenomic databases

HOGENOMHBG665227.
OMAQKIVDDM.

Family and domain databases

HAMAPMF_00163. Pep_deformylase.
[Tree]
InterProIPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view]
Gene3DG3DSA:3.90.45.10. Fmet_deformylase. 1 hit.
KOK01462.
PANTHERPTHR10458. Fmet_deformylase. 1 hit.
PfamPF01327. Pep_deformylase. 1 hit.
[Graphical view]
PIRSFPIRSF004749. Pep_def. 1 hit.
PRINTSPR01576. PDEFORMYLASE.
SUPFAMSSF56420. Fmet_deformylase. 1 hit.
TIGRFAMsTIGR00079. Pept_deformyl. 1 hit.
ProtoNetSearch...

Entry information

Entry nameDEF_PHEZH
AccessionPrimary (citable) accession number: B4RDT8
Entry history
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: September 23, 2008
Last modified: January 25, 2012
This is version 26 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

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