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Reviewed, UniProtKB/Swiss-Prot Q9HBH1 (DEFM_HUMAN)

Last modified November 3, 2009. Version 68. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data | Customize display text xml rdf/xml gff fasta
Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein namesRecommended name:
    Peptide deformylase, mitochondrial
    EC=3.5.1.88
Alternative name(s):
    Polypeptide deformylase
Gene names
Name: PDF
Synonyms: PDF1A
OrganismHomo sapiens (Human) [Complete proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

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Protein attributes

Sequence length243 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level.

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General annotation (Comments)

Function

Removes the formyl group from the N-terminal Met of newly synthesized proteins By similarity.

Catalytic activity

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

Cofactor

Binds 1 Fe2+ ion By similarity.

Subcellular location

Mitochondrion Potential.

Tissue specificity

Ubiquitous.

Sequence similarities

Belongs to the polypeptide deformylase family.

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Ontologies

Keywords
   Biological processProtein biosynthesis
   Cellular componentMitochondrion
   Coding sequence diversityPolymorphism
   DomainTransit peptide
   LigandIron
Metal-binding
   Molecular functionHydrolase
   Technical term3D-structure
Complete proteome
Gene Ontology (GO)
   Biological processN-terminal protein amino acid modification

Inferred from direct assay. Source: HGNC

peptidyl-methionine modification

Inferred from direct assay. Source: HGNC

positive regulation of cell proliferation

Inferred from mutant phenotype. Source: HGNC

translation

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular componentmitochondrion

Inferred from direct assay. Source: HGNC

   Molecular functioniron ion binding

Inferred from electronic annotation. Source: UniProtKB-KW

peptide deformylase activity

Inferred from direct assay. Source: HGNC

Complete GO annotation...

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Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Transit peptide1 – 3939Mitochondrion Probable
Chain40 – 243204Peptide deformylase, mitochondrial
PRO_0000006729

Sites

Active site2151 By similarity
Metal binding1721Iron By similarity
Metal binding2141Iron By similarity
Metal binding2181Iron By similarity

Natural variations

Natural variant111W → R: dbSNP rs8057004. Ref.3
VAR_060122

Secondary structure

1 ............................. 243
Helix Strand Turn

Details...

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Sequences

Sequence LengthMass (Da)Tools
Q9HBH1-1 [UniParc].

Last modified March 1, 2001. Version 1.
Checksum: B15A3456F0F8D689

FASTA24327,013
        10         20         30         40         50         60 
MARLWGALSL WPLWAAVPWG GAAAVGVRAC SSTAAPDGVE GPALRRSYWR HLRRLVLGPP 

        70         80         90        100        110        120 
EPPFSHVCQV GDPVLRGVAA PVERAQLGGP ELQRLTQRLV QVMRRRRCVG LSAPQLGVPR 

       130        140        150        160        170        180 
QVLALELPEA LCRECPPRQR ALRQMEPFPL RVFVNPSLRV LDSRLVTFPE GCESVAGFLA 

       190        200        210        220        230        240 
CVPRFQAVQI SGLDPNGEQV VWQASGWAAR IIQHEMDHLQ GCLFIDKMDS RTFTNVYWMK 


VND

« Hide

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References

« Hide 'large scale' references
[1]"Identification of eukaryotic peptide deformylases reveals universality of N-terminal protein processing mechanisms."
Giglione C., Serero A., Pierre M., Boisson B., Meinnel T.
EMBO J. 19:5916-5929(2000) [PubMed: 11060042] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]"A human homolog of bacterial peptide deformylases."
Lonetto M.A., Zhu Y., Li X., Southan C.
Submitted (NOV-2000) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[3]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed: 15489334] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANT ARG-11.
Tissue: Placenta.
[4]"An unusual peptide deformylase features in the human mitochondrial N-terminal methionine excision pathway."
Serero A., Giglione C., Sardini A., Martinez-Sanz J., Meinnel T.
J. Biol. Chem. 278:52953-52963(2003) [PubMed: 14532271] [Abstract]
Cited for: MITOCHONDRIAL TRANSIT PEPTIDE.
+Additional computationally mapped references.

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Cross-references

Sequence databases

AF239156 mRNA. Translation: AAG33968.1.
AF322879 mRNA. Translation: AAK15624.1.
BC019912 mRNA. Translation: AAH19912.1.
IPIIPI00007060.
RefSeqNP_071736.1.
UniGeneHs.130849

3D structure databases

EntryMethodResolution (Å)ChainPositionsPDBsum
3G5KX-ray1.70A/B/C/D64-243[»]
3G5PX-ray1.70A/B/C/D64-243[»]
ModBaseSearch...

Protein-protein interaction databases

STRINGQ9HBH1.

Proteomic databases

PeptideAtlasQ9HBH1.
PRIDEQ9HBH1.

Genome annotation databases

EnsemblENST00000288022; ENSP00000288022; ENSG00000157312; Homo sapiens. [Genome view]
GeneID64146.
KEGGhsa:64146.
NMPDRfig|9606.3.peg.12472.
UCSCuc002ewx.1. human.

Organism-specific databases

CTD64146.
GeneCardsGC16M067920.
HGNCHGNC:30012. PDF.
GenAtlasSearch...

Phylogenomic databases

HOVERGENQ9HBH1.
OMALYPSRIT.

Enzyme and pathway databases

BRENDA3.5.1.88. 247.

Gene expression databases

ArrayExpressQ9HBH1.
BgeeQ9HBH1.
GenevestigatorQ9HBH1.
GermOnlineENSG00000157312. Homo sapiens.

Family and domain databases

InterProIPR000181. Fmet_deformylase.
[Graphical view]
Gene3DG3DSA:3.90.45.10. Fmet_deformylase. 1 hit.
PANTHERPTHR10458. Fmet_deformylase. 1 hit.
PfamPF01327. Pep_deformylase. 1 hit.
[Graphical view]
PRINTSPR01576. PDEFORMYLASE.
ProDomPD003844. Fmet_deformylase. 1 hit.
[Graphical view] [Entries sharing at least one domain]
ProtoNetSearch...

Other Resources

NextBio66046.

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Entry information

Entry nameDEFM_HUMAN
AccessionPrimary (citable) accession number: Q9HBH1
Secondary accession number(s): Q8WUN6
Entry history
Integrated into UniProtKB/Swiss-Prot: December 5, 2001
Last sequence update: March 1, 2001
Last modified: November 3, 2009
This is version 68 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation projectHPI (Human Proteome Initiative)
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

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Human chromosome 16: entries, gene names and cross-references to MIM

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List of human entries with polymorphisms or disease mutations

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents