Q9HBH1 (DEFM_HUMAN) Reviewed, UniProtKB/Swiss-Prot

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) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › 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
Coding sequence diversity	Polymorphism
Domain	Transit peptide
Ligand	Iron Metal-binding
Molecular function	Hydrolase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	N-terminal protein amino acid modification Inferred from direct assay PubMed 15489958. Source: HGNC peptidyl-methionine modification Inferred from direct assay PubMed 15489958. Source: HGNC positive regulation of cell proliferation Inferred from mutant phenotype PubMed 15489958. Source: HGNC translation Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	mitochondrion Inferred from direct assay PubMed 15489958. Source: HGNC
Molecular_function	iron ion binding Inferred from electronic annotation. Source: InterPro peptide deformylase activity Inferred from direct assay PubMed 15489958. 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

Natural variations

Natural variant

11

1

W → R. Ref.3
Corresponds to variant rs8057004 [ dbSNP | Ensembl ].

VAR_060122

Secondary structure

1

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243

Helix Strand Turn

Details...

Helix

73 – 75

3

Helix

84 – 86

3

Helix

90 – 105

16

Beta strand

109 – 112

4

Helix

113 – 116

4

Beta strand

120 – 127

8

Helix

129 – 133

5

Helix

137 – 143

7

Beta strand

148 – 170

23

Beta strand

178 – 193

16

Beta strand

199 – 205

7

Helix

206 – 219

14

Helix

224 – 226

3

Helix

230 – 232

3

Sequences

	Sequence		Length	Mass (Da)
	Q9HBH1 [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] [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: MITOCHONDRIAL TRANSIT PEPTIDE.
[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].
+	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.

IPI

IPI00007060.

RefSeq

NP_071736.1. NM_022341.1.

UniGene

Hs.130849.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

Q9HBH1.

ModBase

Search...

Protein-protein interaction databases

STRING

9606.ENSP00000305459.

Polymorphism databases

DMDM

17433054.

Proteomic databases

PeptideAtlas

Q9HBH1.

PRIDE

Q9HBH1.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000288022; ENSP00000288022; ENSG00000258429.

GeneID

64146.

KEGG

hsa:64146.

UCSC

uc002ewx.1. human.

Organism-specific databases

CTD

64146.

GeneCards

GC16M069362.

H-InvDB

HIX0013187.

HGNC

HGNC:30012. PDF.

neXtProt

NX_Q9HBH1.

PharmGKB

PA144596394.

GenAtlas

Search...

Phylogenomic databases

HOGENOM

HOG000243508.

HOVERGEN

HBG018948.

InParanoid

Q9HBH1.

KO

K01462.

OMA

MDSRTFT.

Enzyme and pathway databases

SABIO-RK

Q9HBH1.

Gene expression databases

Bgee

Q9HBH1.

Genevestigator

Q9HBH1.

GermOnline

ENSG00000157312. Homo sapiens.

Family and domain databases

Gene3D

3.90.45.10. 1 hit.

InterPro

IPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view]

PANTHER

PTHR10458. PTHR10458. 1 hit.

Pfam

PF01327. Pep_deformylase. 1 hit.
[Graphical view]

PRINTS

PR01576. PDEFORMYLASE.

SUPFAM

SSF56420. Fmet_deformylase. 1 hit.

ProtoNet

Search...

Other

BindingDB

Q9HBH1.

ChEMBL

CHEMBL4647.

EvolutionaryTrace

Q9HBH1.

GenomeRNAi

64146.

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:	May 1, 2013
This is version 97 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.