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Protein

Peptide deformylase, mitochondrial

Gene

PDF

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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

Catalytic activityi

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

Cofactori

Co2+1 PublicationNote: Binds 1 Co2+ ion.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei71 – 711Substrate; via carbonyl oxygen
Binding sitei169 – 1691Substrate; via carbonyl oxygen
Binding sitei171 – 1711Substrate; via amide nitrogen
Metal bindingi172 – 1721Cobalt; catalytic
Metal bindingi214 – 2141Cobalt; catalytic
Active sitei215 – 2151By similarity
Metal bindingi218 – 2181Cobalt; catalytic

GO - Molecular functioni

  • iron ion binding Source: InterPro
  • peptide deformylase activity Source: HGNC

GO - Biological processi

  • co-translational protein modification Source: GO_Central
  • N-terminal protein amino acid modification Source: HGNC
  • peptidyl-methionine modification Source: HGNC
  • positive regulation of cell proliferation Source: HGNC
  • translation Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

Cobalt, Metal-binding

Enzyme and pathway databases

BRENDAi3.5.1.88. 2681.
SABIO-RKQ9HBH1.

Names & Taxonomyi

Protein namesi
Recommended name:
Peptide deformylase, mitochondrial (EC:3.5.1.88)
Alternative name(s):
Polypeptide deformylase
Gene namesi
Name:PDF
Synonyms:PDF1A
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 16

Organism-specific databases

HGNCiHGNC:30012. PDF.

Subcellular locationi

GO - Cellular componenti

  • mitochondrion Source: HGNC
Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA144596394.

Polymorphism and mutation databases

BioMutaiPDF.
DMDMi17433054.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 3939Mitochondrion1 PublicationAdd
BLAST
Chaini40 – 243204Peptide deformylase, mitochondrialPRO_0000006729Add
BLAST

Proteomic databases

MaxQBiQ9HBH1.
PeptideAtlasiQ9HBH1.
PRIDEiQ9HBH1.

Expressioni

Tissue specificityi

Ubiquitous.

Gene expression databases

BgeeiQ9HBH1.
ExpressionAtlasiQ9HBH1. baseline.
GenevestigatoriQ9HBH1.

Organism-specific databases

HPAiHPA063409.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

BioGridi122085. 10 interactions.
STRINGi9606.ENSP00000305459.

Structurei

Secondary structure

1
243
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi73 – 753Combined sources
Helixi84 – 863Combined sources
Helixi90 – 10516Combined sources
Beta strandi109 – 1124Combined sources
Helixi113 – 1164Combined sources
Beta strandi120 – 1278Combined sources
Helixi129 – 1335Combined sources
Helixi137 – 1437Combined sources
Beta strandi148 – 17023Combined sources
Beta strandi178 – 19316Combined sources
Beta strandi199 – 2057Combined sources
Helixi206 – 21914Combined sources
Helixi224 – 2263Combined sources
Helixi230 – 2323Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3G5KX-ray1.70A/B/C/D64-243[»]
3G5PX-ray1.70A/B/C/D64-243[»]
ProteinModelPortaliQ9HBH1.
SMRiQ9HBH1. Positions 64-243.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9HBH1.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni165 – 17511Hydrophobic dimerization interfaceAdd
BLAST

Sequence similaritiesi

Belongs to the polypeptide deformylase family.Curated

Keywords - Domaini

Transit peptide

Phylogenomic databases

GeneTreeiENSGT00390000018698.
HOGENOMiHOG000243508.
HOVERGENiHBG018948.
InParanoidiQ9HBH1.
KOiK01462.
OMAiTFTNIHW.
OrthoDBiEOG75B86Q.
TreeFamiTF323637.

Family and domain databases

Gene3Di3.90.45.10. 1 hit.
HAMAPiMF_00163. Pep_deformylase.
InterProiIPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view]
PANTHERiPTHR10458. PTHR10458. 1 hit.
PfamiPF01327. Pep_deformylase. 1 hit.
[Graphical view]
PRINTSiPR01576. PDEFORMYLASE.
SUPFAMiSSF56420. SSF56420. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q9HBH1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MARLWGALSL WPLWAAVPWG GAAAVGVRAC SSTAAPDGVE GPALRRSYWR
60 70 80 90 100
HLRRLVLGPP EPPFSHVCQV GDPVLRGVAA PVERAQLGGP ELQRLTQRLV
110 120 130 140 150
QVMRRRRCVG LSAPQLGVPR QVLALELPEA LCRECPPRQR ALRQMEPFPL
160 170 180 190 200
RVFVNPSLRV LDSRLVTFPE GCESVAGFLA CVPRFQAVQI SGLDPNGEQV
210 220 230 240
VWQASGWAAR IIQHEMDHLQ GCLFIDKMDS RTFTNVYWMK VND
Length:243
Mass (Da):27,013
Last modified:March 1, 2001 - v1
Checksum:iB15A3456F0F8D689
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti11 – 111W → R.1 Publication
Corresponds to variant rs8057004 [ dbSNP | Ensembl ].
VAR_060122

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF239156 mRNA. Translation: AAG33968.1.
AF322879 mRNA. Translation: AAK15624.1.
BC019912 mRNA. Translation: AAH19912.1.
CCDSiCCDS10875.1.
RefSeqiNP_071736.1. NM_022341.1.
UniGeneiHs.130849.

Genome annotation databases

EnsembliENST00000288022; ENSP00000288022; ENSG00000258429.
GeneIDi64146.
KEGGihsa:64146.
UCSCiuc002ewx.1. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF239156 mRNA. Translation: AAG33968.1.
AF322879 mRNA. Translation: AAK15624.1.
BC019912 mRNA. Translation: AAH19912.1.
CCDSiCCDS10875.1.
RefSeqiNP_071736.1. NM_022341.1.
UniGeneiHs.130849.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3G5KX-ray1.70A/B/C/D64-243[»]
3G5PX-ray1.70A/B/C/D64-243[»]
ProteinModelPortaliQ9HBH1.
SMRiQ9HBH1. Positions 64-243.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi122085. 10 interactions.
STRINGi9606.ENSP00000305459.

Chemistry

BindingDBiQ9HBH1.
ChEMBLiCHEMBL4647.

Polymorphism and mutation databases

BioMutaiPDF.
DMDMi17433054.

Proteomic databases

MaxQBiQ9HBH1.
PeptideAtlasiQ9HBH1.
PRIDEiQ9HBH1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000288022; ENSP00000288022; ENSG00000258429.
GeneIDi64146.
KEGGihsa:64146.
UCSCiuc002ewx.1. human.

Organism-specific databases

CTDi64146.
GeneCardsiGC16M069362.
H-InvDBHIX0013187.
HGNCiHGNC:30012. PDF.
HPAiHPA063409.
neXtProtiNX_Q9HBH1.
PharmGKBiPA144596394.
GenAtlasiSearch...

Phylogenomic databases

GeneTreeiENSGT00390000018698.
HOGENOMiHOG000243508.
HOVERGENiHBG018948.
InParanoidiQ9HBH1.
KOiK01462.
OMAiTFTNIHW.
OrthoDBiEOG75B86Q.
TreeFamiTF323637.

Enzyme and pathway databases

BRENDAi3.5.1.88. 2681.
SABIO-RKQ9HBH1.

Miscellaneous databases

ChiTaRSiPDF. human.
EvolutionaryTraceiQ9HBH1.
GeneWikiiPDF_(gene).
GenomeRNAii64146.
NextBioi66046.
PROiQ9HBH1.

Gene expression databases

BgeeiQ9HBH1.
ExpressionAtlasiQ9HBH1. baseline.
GenevestigatoriQ9HBH1.

Family and domain databases

Gene3Di3.90.45.10. 1 hit.
HAMAPiMF_00163. Pep_deformylase.
InterProiIPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view]
PANTHERiPTHR10458. PTHR10458. 1 hit.
PfamiPF01327. Pep_deformylase. 1 hit.
[Graphical view]
PRINTSiPR01576. PDEFORMYLASE.
SUPFAMiSSF56420. SSF56420. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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. 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.

Entry informationi

Entry nameiDEFM_HUMAN
AccessioniPrimary (citable) accession number: Q9HBH1
Secondary accession number(s): Q8WUN6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 5, 2001
Last sequence update: March 1, 2001
Last modified: May 27, 2015
This is version 116 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (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.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 16
    Human chromosome 16: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  5. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.