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Q9HBH1 (DEFM_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 105. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

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) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

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

General annotation (Comments)

Function

Removes the formyl group from the N-terminal Met of newly synthesized proteins By similarity. HAMAP-Rule MF_00163

Catalytic activity

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

Cofactor

Binds 1 Co2+ ion Probable. Ref.6

Subunit structure

Homodimer. Ref.6

Subcellular location

Mitochondrion Potential HAMAP-Rule MF_00163.

Tissue specificity

Ubiquitous.

Sequence similarities

Belongs to the polypeptide deformylase family.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Transit peptide1 – 3939Mitochondrion Probable
Chain40 – 243204Peptide deformylase, mitochondrial HAMAP-Rule MF_00163
PRO_0000006729

Regions

Region165 – 17511Hydrophobic dimerization interface HAMAP-Rule MF_00163

Sites

Active site2151 By similarity
Metal binding1721Cobalt; catalytic
Metal binding2141Cobalt; catalytic
Metal binding2181Cobalt; catalytic
Binding site711Substrate; via carbonyl oxygen
Binding site1691Substrate; via carbonyl oxygen
Binding site1711Substrate; via amide nitrogen

Natural variations

Natural variant111W → R. Ref.3
Corresponds to variant rs8057004 [ dbSNP | Ensembl ].
VAR_060122

Secondary structure

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

Details...

Sequences

Sequence LengthMass (Da)Tools
Q9HBH1 [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

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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [Abstract]
Cited for: TRANSIT PEPTIDE CLEAVAGE SITE.
[5]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[6]"Structure and activity of human mitochondrial peptide deformylase, a novel cancer target."
Escobar-Alvarez S., Goldgur Y., Yang G., Ouerfelli O., Li Y., Scheinberg D.A.
J. Mol. Biol. 387:1211-1228(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 64-243 IN COMPLEX WITH SUBSTRATE ANALOG AND COBALT ION, COFACTOR, METAL-BINDING SITES, SUBSTRATE-BINDING SITES, SUBUNIT.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AF239156 mRNA. Translation: AAG33968.1.
AF322879 mRNA. Translation: AAK15624.1.
BC019912 mRNA. Translation: AAH19912.1.
RefSeqNP_071736.1. NM_022341.1.
UniGeneHs.130849.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3G5KX-ray1.70A/B/C/D64-243[»]
3G5PX-ray1.70A/B/C/D64-243[»]
ProteinModelPortalQ9HBH1.
SMRQ9HBH1. Positions 64-243.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING9606.ENSP00000305459.

Chemistry

BindingDBQ9HBH1.
ChEMBLCHEMBL4647.

Polymorphism databases

DMDM17433054.

Proteomic databases

PeptideAtlasQ9HBH1.
PRIDEQ9HBH1.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000288022; ENSP00000288022; ENSG00000258429.
GeneID64146.
KEGGhsa:64146.
UCSCuc002ewx.1. human.

Organism-specific databases

CTD64146.
GeneCardsGC16M069362.
H-InvDBHIX0013187.
HGNCHGNC:30012. PDF.
neXtProtNX_Q9HBH1.
PharmGKBPA144596394.
GenAtlasSearch...

Phylogenomic databases

HOGENOMHOG000243508.
HOVERGENHBG018948.
InParanoidQ9HBH1.
KOK01462.
OMARVCQVGD.
OrthoDBEOG75B86Q.
TreeFamTF323637.

Enzyme and pathway databases

SABIO-RKQ9HBH1.

Gene expression databases

BgeeQ9HBH1.
GenevestigatorQ9HBH1.

Family and domain databases

Gene3D3.90.45.10. 1 hit.
HAMAPMF_00163. Pep_deformylase.
InterProIPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view]
PANTHERPTHR10458. PTHR10458. 1 hit.
PfamPF01327. Pep_deformylase. 1 hit.
[Graphical view]
PRINTSPR01576. PDEFORMYLASE.
SUPFAMSSF56420. SSF56420. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceQ9HBH1.
GeneWikiPDF_(gene).
GenomeRNAi64146.
NextBio66046.
PROQ9HBH1.

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: April 16, 2014
This is version 105 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 16

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