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Q9HBH1

- DEFM_HUMAN

UniProt

Q9HBH1 - DEFM_HUMAN

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Protein
Peptide deformylase, mitochondrial
Gene
PDF, PDF1A
Organism
Homo sapiens (Human)
Status
Reviewed - 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.UniRule annotation

Catalytic activityi

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

Cofactori

Binds 1 Co2+ ion Inferred.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 – 2151 By similarity
Metal bindingi218 – 2181Cobalt; catalytic

GO - Molecular functioni

  1. iron ion binding Source: InterPro
  2. peptide deformylase activity Source: HGNC

GO - Biological processi

  1. N-terminal protein amino acid modification Source: HGNC
  2. peptidyl-methionine modification Source: HGNC
  3. positive regulation of cell proliferation Source: HGNC
  4. 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

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: Chromosome 16

Organism-specific databases

HGNCiHGNC:30012. PDF.

Subcellular locationi

Mitochondrion Reviewed prediction UniRule annotation

GO - Cellular componenti

  1. mitochondrion Source: HGNC
Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA144596394.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 3939Mitochondrion Inferred
Add
BLAST
Chaini40 – 243204Peptide deformylase, mitochondrialUniRule annotation
PRO_0000006729Add
BLAST

Proteomic databases

MaxQBiQ9HBH1.
PeptideAtlasiQ9HBH1.
PRIDEiQ9HBH1.

Expressioni

Tissue specificityi

Ubiquitous.

Gene expression databases

BgeeiQ9HBH1.
GenevestigatoriQ9HBH1.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

STRINGi9606.ENSP00000305459.

Structurei

Secondary structure

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

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiQ9HBH1.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni165 – 17511Hydrophobic dimerization interfaceUniRule annotation
Add
BLAST

Sequence similaritiesi

Keywords - Domaini

Transit peptide

Phylogenomic databases

HOGENOMiHOG000243508.
HOVERGENiHBG018948.
InParanoidiQ9HBH1.
KOiK01462.
OMAiRVCQVGD.
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

MARLWGALSL WPLWAAVPWG GAAAVGVRAC SSTAAPDGVE GPALRRSYWR    50
HLRRLVLGPP EPPFSHVCQV GDPVLRGVAA PVERAQLGGP ELQRLTQRLV 100
QVMRRRRCVG LSAPQLGVPR QVLALELPEA LCRECPPRQR ALRQMEPFPL 150
RVFVNPSLRV LDSRLVTFPE GCESVAGFLA CVPRFQAVQI SGLDPNGEQV 200
VWQASGWAAR IIQHEMDHLQ GCLFIDKMDS RTFTNVYWMK VND 243
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:
EMBL
GenBank
DDBJ
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.

Polymorphism databases

DMDMi17433054.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AF239156 mRNA. Translation: AAG33968.1 .
AF322879 mRNA. Translation: AAK15624.1 .
BC019912 mRNA. Translation: AAH19912.1 .
CCDSi CCDS10875.1.
RefSeqi NP_071736.1. NM_022341.1.
UniGenei Hs.130849.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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 [» ]
ProteinModelPortali Q9HBH1.
SMRi Q9HBH1. Positions 64-243.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 9606.ENSP00000305459.

Chemistry

BindingDBi Q9HBH1.
ChEMBLi CHEMBL4647.

Polymorphism databases

DMDMi 17433054.

Proteomic databases

MaxQBi Q9HBH1.
PeptideAtlasi Q9HBH1.
PRIDEi Q9HBH1.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000288022 ; ENSP00000288022 ; ENSG00000258429 .
GeneIDi 64146.
KEGGi hsa:64146.
UCSCi uc002ewx.1. human.

Organism-specific databases

CTDi 64146.
GeneCardsi GC16M069362.
H-InvDB HIX0013187.
HGNCi HGNC:30012. PDF.
neXtProti NX_Q9HBH1.
PharmGKBi PA144596394.
GenAtlasi Search...

Phylogenomic databases

HOGENOMi HOG000243508.
HOVERGENi HBG018948.
InParanoidi Q9HBH1.
KOi K01462.
OMAi RVCQVGD.
OrthoDBi EOG75B86Q.
TreeFami TF323637.

Enzyme and pathway databases

SABIO-RK Q9HBH1.

Miscellaneous databases

EvolutionaryTracei Q9HBH1.
GeneWikii PDF_(gene).
GenomeRNAii 64146.
NextBioi 66046.
PROi Q9HBH1.

Gene expression databases

Bgeei Q9HBH1.
Genevestigatori Q9HBH1.

Family and domain databases

Gene3Di 3.90.45.10. 1 hit.
HAMAPi MF_00163. Pep_deformylase.
InterProi IPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view ]
PANTHERi PTHR10458. PTHR10458. 1 hit.
Pfami PF01327. Pep_deformylase. 1 hit.
[Graphical view ]
PRINTSi PR01576. PDEFORMYLASE.
SUPFAMi SSF56420. SSF56420. 1 hit.
ProtoNeti Search...

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: July 9, 2014
This is version 107 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

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