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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)DescriptionActionsGraphical viewLength
Binding sitei71Substrate; via carbonyl oxygen1
Binding sitei169Substrate; via carbonyl oxygen1
Binding sitei171Substrate; via amide nitrogen1
Metal bindingi172Cobalt; catalytic1
Metal bindingi214Cobalt; catalytic1
Active sitei215By similarity1
Metal bindingi218Cobalt; catalytic1

GO - Molecular functioni

  • metal ion binding Source: UniProtKB-KW
  • peptide deformylase activity Source: HGNC

GO - Biological processi

  • 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

BioCyciZFISH:HS08199-MONOMER.
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
Proteomesi
  • UP000005640 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

DisGeNETi64146.
OpenTargetsiENSG00000258429.
PharmGKBiPA144596394.

Chemistry databases

ChEMBLiCHEMBL4647.

Polymorphism and mutation databases

BioMutaiPDF.
DMDMi17433054.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transit peptidei1 – 39Mitochondrion1 PublicationAdd BLAST39
ChainiPRO_000000672940 – 243Peptide deformylase, mitochondrialAdd BLAST204

Proteomic databases

EPDiQ9HBH1.
MaxQBiQ9HBH1.
PaxDbiQ9HBH1.
PeptideAtlasiQ9HBH1.
PRIDEiQ9HBH1.

Expressioni

Tissue specificityi

Ubiquitous.

Gene expression databases

BgeeiENSG00000258429.
ExpressionAtlasiQ9HBH1. baseline and differential.
GenevisibleiQ9HBH1. HS.

Organism-specific databases

HPAiHPA063409.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

BioGridi122085. 47 interactors.
IntActiQ9HBH1. 25 interactors.
STRINGi9606.ENSP00000288022.

Chemistry databases

BindingDBiQ9HBH1.

Structurei

Secondary structure

1243
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi73 – 75Combined sources3
Helixi84 – 86Combined sources3
Helixi90 – 105Combined sources16
Beta strandi109 – 112Combined sources4
Helixi113 – 116Combined sources4
Beta strandi120 – 127Combined sources8
Helixi129 – 133Combined sources5
Helixi137 – 143Combined sources7
Beta strandi148 – 170Combined sources23
Beta strandi178 – 193Combined sources16
Beta strandi199 – 205Combined sources7
Helixi206 – 219Combined sources14
Helixi224 – 226Combined sources3
Helixi230 – 232Combined sources3

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiQ9HBH1.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni165 – 175Hydrophobic dimerization interfaceAdd BLAST11

Sequence similaritiesi

Belongs to the polypeptide deformylase family.Curated

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiKOG3137. Eukaryota.
COG0242. LUCA.
GeneTreeiENSGT00390000018698.
HOGENOMiHOG000243508.
HOVERGENiHBG018948.
InParanoidiQ9HBH1.
KOiK01462.
OMAiILQHEMD.
OrthoDBiEOG091G0JOY.
TreeFamiTF323637.

Family and domain databases

CDDicd00487. Pep_deformylase. 1 hit.
Gene3Di3.90.45.10. 1 hit.
HAMAPiMF_00163. Pep_deformylase. 1 hit.
InterProiIPR023635. 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)DescriptionActionsGraphical viewLength
Natural variantiVAR_06012211W → R.1 PublicationCorresponds to variant rs8057004dbSNPEnsembl.1

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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3G5KX-ray1.70A/B/C/D64-243[»]
3G5PX-ray1.70A/B/C/D64-243[»]
ProteinModelPortaliQ9HBH1.
SMRiQ9HBH1.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi122085. 47 interactors.
IntActiQ9HBH1. 25 interactors.
STRINGi9606.ENSP00000288022.

Chemistry databases

BindingDBiQ9HBH1.
ChEMBLiCHEMBL4647.

Polymorphism and mutation databases

BioMutaiPDF.
DMDMi17433054.

Proteomic databases

EPDiQ9HBH1.
MaxQBiQ9HBH1.
PaxDbiQ9HBH1.
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.
DisGeNETi64146.
GeneCardsiPDF.
H-InvDBHIX0013187.
HGNCiHGNC:30012. PDF.
HPAiHPA063409.
neXtProtiNX_Q9HBH1.
OpenTargetsiENSG00000258429.
PharmGKBiPA144596394.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3137. Eukaryota.
COG0242. LUCA.
GeneTreeiENSGT00390000018698.
HOGENOMiHOG000243508.
HOVERGENiHBG018948.
InParanoidiQ9HBH1.
KOiK01462.
OMAiILQHEMD.
OrthoDBiEOG091G0JOY.
TreeFamiTF323637.

Enzyme and pathway databases

BioCyciZFISH:HS08199-MONOMER.
BRENDAi3.5.1.88. 2681.
SABIO-RKQ9HBH1.

Miscellaneous databases

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

Gene expression databases

BgeeiENSG00000258429.
ExpressionAtlasiQ9HBH1. baseline and differential.
GenevisibleiQ9HBH1. HS.

Family and domain databases

CDDicd00487. Pep_deformylase. 1 hit.
Gene3Di3.90.45.10. 1 hit.
HAMAPiMF_00163. Pep_deformylase. 1 hit.
InterProiIPR023635. Peptide_deformylase.
[Graphical view]
PANTHERiPTHR10458. PTHR10458. 1 hit.
PfamiPF01327. Pep_deformylase. 1 hit.
[Graphical view]
PRINTSiPR01576. PDEFORMYLASE.
SUPFAMiSSF56420. SSF56420. 1 hit.
ProtoNetiSearch...

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: November 2, 2016
This is version 130 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

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 one 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.