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Q9HBH1

- DEFM_HUMAN

UniProt

Q9HBH1 - DEFM_HUMAN

Protein

Peptide deformylase, mitochondrial

Gene

PDF

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 108 (01 Oct 2014)
      Sequence version 1 (01 Mar 2001)
      Previous versions | rss
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    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

    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

    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

    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

    GO - Cellular componenti

    1. mitochondrion Source: HGNC

    Keywords - Cellular componenti

    Mitochondrion

    Pathology & Biotechi

    Organism-specific databases

    PharmGKBiPA144596394.

    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.
    GenevestigatoriQ9HBH1.

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Protein-protein interaction databases

    STRINGi9606.ENSP00000305459.

    Structurei

    Secondary structure

    1
    243
    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.
    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

    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

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    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

    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: October 1, 2014
    This is version 108 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