Reviewed, UniProtKB/Swiss-Prot Q9HBH1 (DEFM_HUMAN)

Names and origin

Protein names

Recommended name:
    Peptide deformylase, mitochondrial
    EC=3.5.1.88
Alternative name(s):
    Polypeptide deformylase

Gene names

Name:	PDF
Synonyms:	PDF1A

Organism

Homo sapiens (Human)

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	243 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

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.

Ontologies

Keywords
Biological process	Protein biosynthesis
Cellular component	Mitochondrion
Domain	Transit peptide
Ligand	Iron Metal-binding
Molecular function	Hydrolase
Technical term	3D-structure
Gene Ontology (GO)
Biological process	N-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 component	mitochondrion Inferred from direct assay. Source: HGNC
Molecular function	iron ion binding Inferred from electronic annotation. Source: UniProtKB-KW peptide deformylase activity Inferred from direct assay. Source: HGNC
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Transit peptide	1 – 39	39	Mitochondrion Probable
	Chain	40 – 243	204	Peptide deformylase, mitochondrial		PRO_0000006729
Sites
	Active site	215	1	By similarity
	Metal binding	172	1	Iron By similarity
	Metal binding	214	1	Iron By similarity
	Metal binding	218	1	Iron By similarity
Experimental info
	Sequence conflict	11	1	W → R in AAH19912. Ref.3

Sequences

	Sequence		Length	Mass (Da)
	Q9HBH1-1 [UniParc]. Last modified March 1, 2001. Version 1. Checksum: B15A3456F0F8D689	FASTA	243	27,013
	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

References

	« Hide 'large scale' referencesShow '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]. 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.

Cross-references

Sequence databases

EMBLGenBankDDBJ

AF239156 mRNA. Translation: AAG33968.1.
AF322879 mRNA. Translation: AAK15624.1.
BC019912 mRNA. Translation: AAH19912.1.

IPI

IPI00007060.

RefSeq

NP_071736.1.

UniGene

Hs.130849

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3G5K	X-ray	1.70	A/B/C/D	64-243	[»]
3G5P	X-ray	1.70	A/B/C/D	64-243	[»]

ModBase

Search...

Proteomic databases

PeptideAtlas

Q9HBH1.

PRIDE

Q9HBH1.

Genome annotation databases

Ensembl

ENSG00000157312. Homo sapiens. [Contig view]

GeneID

64146.

KEGG

hsa:64146.

NMPDR

fig|9606.3.peg.12472.

Organism-specific databases

GeneCards

GC16M067920.

HGNC

HGNC:30012. PDF.

GenAtlas

Search...

Phylogenomic databases

HOVERGEN

Q9HBH1.

OMA

Q9HBH1. LYPSRIT.

Enzyme and pathway databases

BRENDA

3.5.1.88. 247.

Gene expression databases

ArrayExpress

Q9HBH1.

Bgee

Q9HBH1.

GermOnline

ENSG00000157312. Homo sapiens.

Family and domain databases

InterPro

IPR000181. Fmet_deformylase.
[Graphical view]

Gene3D

G3DSA:3.90.45.10. Fmet_deformylase. 1 hit.

PANTHER

PTHR10458. Fmet_deformylase. 1 hit.

Pfam

PF01327. Pep_deformylase. 1 hit.
[Graphical view]

PRINTS

PR01576. PDEFORMYLASE.

ProDom

PD003844. Fmet_deformylase. 1 hit.
[Graphical view] [Entries sharing at least one domain]

ProtoNet

Search...

Other Resources

NextBio

66046.

Entry information

Entry name

DEFM_HUMAN

Accession

Primary (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:	June 16, 2009
This is version 63 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)