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Protein

Methionine aminopeptidase 1D, mitochondrial

Gene

METAP1D

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

Functioni

Removes the N-terminal methionine from nascent proteins. The N-terminal methionine is often cleaved when the second residue in the primary sequence is small and uncharged (Met-Ala-, Cys, Gly, Pro, Ser, Thr, or Val). Requires deformylation of the N(alpha)-formylated initiator methionine before it can be hydrolyzed (By similarity). May play a role in colon tumorigenesis.UniRule annotation1 Publication

Catalytic activityi

Release of N-terminal amino acids, preferentially methionine, from peptides and arylamides.UniRule annotation

Cofactori

Co2+UniRule annotation, Zn2+UniRule annotation, Mn2+UniRule annotation, Fe2+UniRule annotationNote: Binds 2 divalent metal cations per subunit. Has a high-affinity and a low affinity metal-binding site. The true nature of the physiological cofactor is under debate. The enzyme is active with cobalt, zinc, manganese or divalent iron ions. Most likely, methionine aminopeptidases function as mononuclear Fe2+-metalloproteases under physiological conditions, and the catalytically relevant metal-binding site has been assigned to the histidine-containing high-affinity site.UniRule annotation

Kineticsi

  1. KM=573 µM for Met-pro-p-nitroanilide (at pH 8)1 Publication

    pH dependencei

    Optimum pH is 7.5-8.0.1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei161SubstrateUniRule annotation1
    Metal bindingi178Divalent metal cation 1UniRule annotation1
    Metal bindingi189Divalent metal cation 1UniRule annotation1
    Metal bindingi189Divalent metal cation 2; catalyticUniRule annotation1
    Metal bindingi252Divalent metal cation 2; catalytic; via tele nitrogenUniRule annotation1
    Binding sitei259SubstrateUniRule annotation1
    Metal bindingi284Divalent metal cation 2; catalyticUniRule annotation1
    Metal bindingi315Divalent metal cation 1UniRule annotation1
    Metal bindingi315Divalent metal cation 2; catalyticUniRule annotation1

    GO - Molecular functioni

    • aminopeptidase activity Source: UniProtKB
    • metal ion binding Source: UniProtKB-HAMAP
    • metalloaminopeptidase activity Source: UniProtKB-HAMAP
    • metalloexopeptidase activity Source: UniProtKB

    GO - Biological processi

    • N-terminal protein amino acid modification Source: HGNC
    • peptidyl-methionine modification Source: HGNC
    • protein initiator methionine removal Source: UniProtKB-HAMAP
    Complete GO annotation...

    Keywords - Molecular functioni

    Aminopeptidase, Hydrolase, Protease

    Keywords - Ligandi

    Metal-binding

    Enzyme and pathway databases

    BioCyciZFISH:HS16143-MONOMER.
    BRENDAi3.4.11.18. 2681.
    SABIO-RKQ6UB28.

    Protein family/group databases

    MEROPSiM24.028.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Methionine aminopeptidase 1D, mitochondrialUniRule annotation (EC:3.4.11.18UniRule annotation)
    Short name:
    MAP 1DUniRule annotation
    Short name:
    MetAP 1DUniRule annotation
    Alternative name(s):
    Methionyl aminopeptidase type 1D, mitochondrial
    Peptidase M 1DUniRule annotation
    Gene namesi
    Name:METAP1D
    Synonyms:MAP1D
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    Proteomesi
    • UP000005640 Componenti: Chromosome 2

    Organism-specific databases

    HGNCiHGNC:32583. METAP1D.

    Subcellular locationi

    • Mitochondrion UniRule annotation1 Publication

    GO - Cellular componenti

    • mitochondrion Source: HGNC
    Complete GO annotation...

    Keywords - Cellular componenti

    Mitochondrion

    Pathology & Biotechi

    Organism-specific databases

    DisGeNETi254042.
    OpenTargetsiENSG00000172878.

    Polymorphism and mutation databases

    BioMutaiMETAP1D.
    DMDMi74710242.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Transit peptidei1 – 19MitochondrionUniRule annotationAdd BLAST19
    ChainiPRO_000031412620 – 335Methionine aminopeptidase 1D, mitochondrialAdd BLAST316

    Proteomic databases

    EPDiQ6UB28.
    MaxQBiQ6UB28.
    PaxDbiQ6UB28.
    PeptideAtlasiQ6UB28.
    PRIDEiQ6UB28.

    PTM databases

    iPTMnetiQ6UB28.
    PhosphoSitePlusiQ6UB28.

    Expressioni

    Tissue specificityi

    Overexpressed in colon cancer cell lines and colon tumors as compared to normal tissues (at protein level).1 Publication

    Gene expression databases

    BgeeiENSG00000172878.
    GenevisibleiQ6UB28. HS.

    Organism-specific databases

    HPAiHPA030298.
    HPA030299.

    Interactioni

    Protein-protein interaction databases

    BioGridi129008. 6 interactors.
    IntActiQ6UB28. 1 interactor.
    STRINGi9606.ENSP00000315152.

    Structurei

    3D structure databases

    ProteinModelPortaliQ6UB28.
    SMRiQ6UB28.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the peptidase M24A family. Methionine aminopeptidase type 1 subfamily.UniRule annotation

    Keywords - Domaini

    Transit peptide

    Phylogenomic databases

    eggNOGiKOG2738. Eukaryota.
    COG0024. LUCA.
    GeneTreeiENSGT00390000002284.
    HOGENOMiHOG000030427.
    HOVERGENiHBG067178.
    InParanoidiQ6UB28.
    KOiK01265.
    OMAiLNHIYLH.
    OrthoDBiEOG091G0F4A.
    PhylomeDBiQ6UB28.
    TreeFamiTF325318.

    Family and domain databases

    CDDicd01086. MetAP1. 1 hit.
    Gene3Di3.90.230.10. 1 hit.
    HAMAPiMF_01974. MetAP_1. 1 hit.
    InterProiIPR000994. Pept_M24.
    IPR001714. Pept_M24_MAP.
    IPR002467. Pept_M24A_MAP1.
    [Graphical view]
    PfamiPF00557. Peptidase_M24. 1 hit.
    [Graphical view]
    PRINTSiPR00599. MAPEPTIDASE.
    SUPFAMiSSF55920. SSF55920. 1 hit.
    TIGRFAMsiTIGR00500. met_pdase_I. 1 hit.
    PROSITEiPS00680. MAP_1. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    Q6UB28-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MAAPSGVHLL VRRGSHRIFS SPLNHIYLHK QSSSQQRRNF FFRRQRDISH
    60 70 80 90 100
    SIVLPAAVSS AHPVPKHIKK PDYVTTGIVP DWGDSIEVKN EDQIQGLHQA
    110 120 130 140 150
    CQLARHVLLL AGKSLKVDMT TEEIDALVHR EIISHNAYPS PLGYGGFPKS
    160 170 180 190 200
    VCTSVNNVLC HGIPDSRPLQ DGDIINIDVT VYYNGYHGDT SETFLVGNVD
    210 220 230 240 250
    ECGKKLVEVA RRCRDEAIAA CRAGAPFSVI GNTISHITHQ NGFQVCPHFV
    260 270 280 290 300
    GHGIGSYFHG HPEIWHHAND SDLPMEEGMA FTIEPIITEG SPEFKVLEDA
    310 320 330
    WTVVSLDNQR SAQFEHTVLI TSRGAQILTK LPHEA
    Length:335
    Mass (Da):37,088
    Last modified:July 5, 2004 - v1
    Checksum:i2EB90946DC983D7B
    GO

    Sequence cautioni

    The sequence AAY55948 differs from that shown. Reason: Erroneous initiation.Curated

    Natural variant

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Natural variantiVAR_05027314G → V.1 PublicationCorresponds to variant rs10497377dbSNPEnsembl.1

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AY374142 mRNA. Translation: AAR27795.1.
    DQ005576 mRNA. Translation: AAY55948.1. Different initiation.
    CH471058 Genomic DNA. Translation: EAX11190.1.
    BC113644 mRNA. Translation: AAI13645.1.
    CCDSiCCDS2246.1.
    RefSeqiNP_001309207.1. NM_001322278.1.
    NP_001309208.1. NM_001322279.1.
    NP_954697.1. NM_199227.2.
    UniGeneiHs.298250.
    Hs.597025.

    Genome annotation databases

    EnsembliENST00000315796; ENSP00000315152; ENSG00000172878.
    GeneIDi254042.
    KEGGihsa:254042.
    UCSCiuc002uhk.4. human.

    Keywords - Coding sequence diversityi

    Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AY374142 mRNA. Translation: AAR27795.1.
    DQ005576 mRNA. Translation: AAY55948.1. Different initiation.
    CH471058 Genomic DNA. Translation: EAX11190.1.
    BC113644 mRNA. Translation: AAI13645.1.
    CCDSiCCDS2246.1.
    RefSeqiNP_001309207.1. NM_001322278.1.
    NP_001309208.1. NM_001322279.1.
    NP_954697.1. NM_199227.2.
    UniGeneiHs.298250.
    Hs.597025.

    3D structure databases

    ProteinModelPortaliQ6UB28.
    SMRiQ6UB28.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi129008. 6 interactors.
    IntActiQ6UB28. 1 interactor.
    STRINGi9606.ENSP00000315152.

    Protein family/group databases

    MEROPSiM24.028.

    PTM databases

    iPTMnetiQ6UB28.
    PhosphoSitePlusiQ6UB28.

    Polymorphism and mutation databases

    BioMutaiMETAP1D.
    DMDMi74710242.

    Proteomic databases

    EPDiQ6UB28.
    MaxQBiQ6UB28.
    PaxDbiQ6UB28.
    PeptideAtlasiQ6UB28.
    PRIDEiQ6UB28.

    Protocols and materials databases

    DNASUi254042.
    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsembliENST00000315796; ENSP00000315152; ENSG00000172878.
    GeneIDi254042.
    KEGGihsa:254042.
    UCSCiuc002uhk.4. human.

    Organism-specific databases

    CTDi254042.
    DisGeNETi254042.
    GeneCardsiMETAP1D.
    HGNCiHGNC:32583. METAP1D.
    HPAiHPA030298.
    HPA030299.
    MIMi610267. gene.
    neXtProtiNX_Q6UB28.
    OpenTargetsiENSG00000172878.
    GenAtlasiSearch...

    Phylogenomic databases

    eggNOGiKOG2738. Eukaryota.
    COG0024. LUCA.
    GeneTreeiENSGT00390000002284.
    HOGENOMiHOG000030427.
    HOVERGENiHBG067178.
    InParanoidiQ6UB28.
    KOiK01265.
    OMAiLNHIYLH.
    OrthoDBiEOG091G0F4A.
    PhylomeDBiQ6UB28.
    TreeFamiTF325318.

    Enzyme and pathway databases

    BioCyciZFISH:HS16143-MONOMER.
    BRENDAi3.4.11.18. 2681.
    SABIO-RKQ6UB28.

    Miscellaneous databases

    ChiTaRSiMETAP1D. human.
    GenomeRNAii254042.
    PROiQ6UB28.
    SOURCEiSearch...

    Gene expression databases

    BgeeiENSG00000172878.
    GenevisibleiQ6UB28. HS.

    Family and domain databases

    CDDicd01086. MetAP1. 1 hit.
    Gene3Di3.90.230.10. 1 hit.
    HAMAPiMF_01974. MetAP_1. 1 hit.
    InterProiIPR000994. Pept_M24.
    IPR001714. Pept_M24_MAP.
    IPR002467. Pept_M24A_MAP1.
    [Graphical view]
    PfamiPF00557. Peptidase_M24. 1 hit.
    [Graphical view]
    PRINTSiPR00599. MAPEPTIDASE.
    SUPFAMiSSF55920. SSF55920. 1 hit.
    TIGRFAMsiTIGR00500. met_pdase_I. 1 hit.
    PROSITEiPS00680. MAP_1. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiMAP12_HUMAN
    AccessioniPrimary (citable) accession number: Q6UB28
    Secondary accession number(s): Q1WNX3
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 15, 2008
    Last sequence update: July 5, 2004
    Last modified: November 30, 2016
    This is version 110 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

    Caution

    It is uncertain whether Met-1 or a Met upstream of this sequence is the initiator.Curated

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Human chromosome 2
      Human chromosome 2: 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. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    5. Peptidase families
      Classification of peptidase families and list of entries
    6. 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.