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Protein

Methionine aminopeptidase

Gene

map

Organism
Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
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).UniRule annotation1 Publication

Catalytic activityi

Release of N-terminal amino acids, preferentially methionine, from peptides and arylamides.UniRule annotation1 Publication

Cofactori

Co2+UniRule annotation1 Publication, Zn2+UniRule annotation1 Publication, Mn2+UniRule annotation1 Publication, Fe2+UniRule annotation1 PublicationNote: 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 annotation1 Publication

Kineticsi

  1. KM=9.2 mM for a Met-Ala-Ser peptide (for the Fe2+-complexed enzyme)2 Publications
  2. KM=11.8 mM for a Met-Ala-Ser peptide (for the Co2+-complexed enzyme)2 Publications
  3. KM=5.0 mM for a Met-Gly-Met-Met peptide (for the Fe2+-complexed enzyme)2 Publications
  4. KM=5.1 mM for a Met-Gly-Met-Met peptide (for the Co2+-complexed enzyme)2 Publications
  5. KM=1.3 mM for a Met-Ser-Ser-His-Arg-Trp-Asp-Trp peptide (for the Fe2+-complexed enzyme)2 Publications
  6. KM=2.0 mM for a Met-Ser-Ser-His-Arg-Trp-Asp-Trp peptide (for the Co2+-complexed enzyme)2 Publications

    pH dependencei

    Optimum pH is 7-8.2 Publications

    Temperature dependencei

    Optimum temperature is about 90 degrees Celsius.2 Publications

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei62 – 621SubstrateUniRule annotation
    Metal bindingi82 – 821Divalent metal cation 1
    Metal bindingi93 – 931Divalent metal cation 1
    Metal bindingi93 – 931Divalent metal cation 2; catalytic
    Metal bindingi153 – 1531Divalent metal cation 2; catalytic; via tele nitrogen
    Binding sitei161 – 1611Substrate
    Metal bindingi187 – 1871Divalent metal cation 2; catalytic
    Metal bindingi280 – 2801Divalent metal cation 1
    Metal bindingi280 – 2801Divalent metal cation 2; catalytic

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Aminopeptidase, Hydrolase, Protease

    Keywords - Ligandi

    Metal-binding

    Enzyme and pathway databases

    BRENDAi3.4.11.18. 5243.

    Protein family/group databases

    MEROPSiM24.035.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Methionine aminopeptidaseUniRule annotation (EC:3.4.11.18UniRule annotation)
    Short name:
    MAPUniRule annotation
    Short name:
    MetAPUniRule annotation
    Alternative name(s):
    Peptidase MUniRule annotation
    Gene namesi
    Name:mapUniRule annotation
    Ordered Locus Names:PF0541
    OrganismiPyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
    Taxonomic identifieri186497 [NCBI]
    Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
    ProteomesiUP000001013 Componenti: Chromosome

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi161 – 1611H → A: Reduces enzymatic activity by 96% at 37 degrees Celsius and by 88% at 87 degrees Celsius; when associated with A-173. 1 Publication
    Mutagenesisi173 – 1731H → A: Reduces enzymatic activity by 96% at 37 degrees Celsius and by 88% at 87 degrees Celsius; when associated with A-161. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 295295Methionine aminopeptidasePRO_0000148978Add
    BLAST

    Proteomic databases

    PRIDEiP56218.

    Interactioni

    Subunit structurei

    Monomer.UniRule annotation2 Publications

    Protein-protein interaction databases

    STRINGi186497.PF0541.

    Structurei

    Secondary structure

    1
    295
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi3 – 2321Combined sources
    Helixi30 – 4314Combined sources
    Beta strandi47 – 504Combined sources
    Beta strandi53 – 564Combined sources
    Beta strandi59 – 613Combined sources
    Beta strandi78 – 8710Combined sources
    Beta strandi90 – 9910Combined sources
    Helixi106 – 12116Combined sources
    Helixi129 – 14012Combined sources
    Turni141 – 1433Combined sources
    Beta strandi148 – 1503Combined sources
    Beta strandi152 – 1543Combined sources
    Beta strandi159 – 1613Combined sources
    Beta strandi165 – 1695Combined sources
    Beta strandi183 – 1864Combined sources
    Beta strandi189 – 1935Combined sources
    Beta strandi197 – 20812Combined sources
    Helixi217 – 22913Combined sources
    Turni230 – 2323Combined sources
    Beta strandi235 – 2373Combined sources
    Helixi238 – 2403Combined sources
    Turni241 – 2433Combined sources
    Helixi246 – 25813Combined sources
    Beta strandi261 – 27010Combined sources
    Beta strandi276 – 2783Combined sources
    Beta strandi280 – 2856Combined sources
    Beta strandi287 – 2926Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1WKMX-ray2.30A/B1-295[»]
    1XGMX-ray2.80A/B1-295[»]
    1XGNX-ray2.90A/B1-295[»]
    1XGOX-ray3.50A1-295[»]
    1XGSX-ray1.75A/B1-295[»]
    2DFIX-ray2.10A/B1-292[»]
    ProteinModelPortaliP56218.
    SMRiP56218. Positions 1-295.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP56218.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the peptidase M24A family. Methionine aminopeptidase archaeal type 2 subfamily.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG0024.
    HOGENOMiHOG000226277.
    KOiK01265.
    OMAiNGHTIEP.

    Family and domain databases

    Gene3Di1.10.10.10. 1 hit.
    3.90.230.10. 2 hits.
    HAMAPiMF_01975. MetAP_2_arc.
    InterProiIPR028595. MetAP_archaeal.
    IPR001714. Pept_M24_MAP.
    IPR000994. Pept_M24_structural-domain.
    IPR002468. Pept_M24A_MAP2.
    IPR018349. Pept_M24A_MAP2_BS.
    IPR011991. WHTH_DNA-bd_dom.
    [Graphical view]
    PANTHERiPTHR10804:SF9. PTHR10804:SF9. 1 hit.
    PfamiPF00557. Peptidase_M24. 1 hit.
    [Graphical view]
    PRINTSiPR00599. MAPEPTIDASE.
    SUPFAMiSSF55920. SSF55920. 2 hits.
    TIGRFAMsiTIGR00501. met_pdase_II. 1 hit.
    PROSITEiPS01202. MAP_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P56218-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MDTEKLMKAG EIAKKVREKA IKLARPGMLL LELAESIEKM IMELGGKPAF
    60 70 80 90 100
    PVNLSINEIA AHYTPYKGDT TVLKEGDYLK IDVGVHIDGF IADTAVTVRV
    110 120 130 140 150
    GMEEDELMEA AKEALNAAIS VARAGVEIKE LGKAIENEIR KRGFKPIVNL
    160 170 180 190 200
    SGHKIERYKL HAGISIPNIY RPHDNYVLKE GDVFAIEPFA TIGAGQVIEV
    210 220 230 240 250
    PPTLIYMYVR DVPVRVAQAR FLLAKIKREY GTLPFAYRWL QNDMPEGQLK
    260 270 280 290
    LALKTLEKAG AIYGYPVLKE IRNGIVAQFE HTIIVEKDSV IVTTE
    Length:295
    Mass (Da):32,842
    Last modified:July 15, 1998 - v1
    Checksum:i9739BC55F812E65B
    GO

    Mass spectrometryi

    Molecular mass is 32848 Da from positions 1 - 295. Determined by ESI. 1 Publication

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AE009950 Genomic DNA. Translation: AAL80665.1.
    PIRiJC5671.
    RefSeqiNP_578270.1. NC_003413.1.
    WP_011011659.1. NC_003413.1.

    Genome annotation databases

    EnsemblBacteriaiAAL80665; AAL80665; PF0541.
    GeneIDi1468383.
    KEGGipfu:PF0541.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AE009950 Genomic DNA. Translation: AAL80665.1.
    PIRiJC5671.
    RefSeqiNP_578270.1. NC_003413.1.
    WP_011011659.1. NC_003413.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1WKMX-ray2.30A/B1-295[»]
    1XGMX-ray2.80A/B1-295[»]
    1XGNX-ray2.90A/B1-295[»]
    1XGOX-ray3.50A1-295[»]
    1XGSX-ray1.75A/B1-295[»]
    2DFIX-ray2.10A/B1-292[»]
    ProteinModelPortaliP56218.
    SMRiP56218. Positions 1-295.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi186497.PF0541.

    Chemistry

    ChEMBLiCHEMBL4857.

    Protein family/group databases

    MEROPSiM24.035.

    Proteomic databases

    PRIDEiP56218.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAL80665; AAL80665; PF0541.
    GeneIDi1468383.
    KEGGipfu:PF0541.

    Phylogenomic databases

    eggNOGiCOG0024.
    HOGENOMiHOG000226277.
    KOiK01265.
    OMAiNGHTIEP.

    Enzyme and pathway databases

    BRENDAi3.4.11.18. 5243.

    Miscellaneous databases

    EvolutionaryTraceiP56218.
    PROiP56218.

    Family and domain databases

    Gene3Di1.10.10.10. 1 hit.
    3.90.230.10. 2 hits.
    HAMAPiMF_01975. MetAP_2_arc.
    InterProiIPR028595. MetAP_archaeal.
    IPR001714. Pept_M24_MAP.
    IPR000994. Pept_M24_structural-domain.
    IPR002468. Pept_M24A_MAP2.
    IPR018349. Pept_M24A_MAP2_BS.
    IPR011991. WHTH_DNA-bd_dom.
    [Graphical view]
    PANTHERiPTHR10804:SF9. PTHR10804:SF9. 1 hit.
    PfamiPF00557. Peptidase_M24. 1 hit.
    [Graphical view]
    PRINTSiPR00599. MAPEPTIDASE.
    SUPFAMiSSF55920. SSF55920. 2 hits.
    TIGRFAMsiTIGR00501. met_pdase_II. 1 hit.
    PROSITEiPS01202. MAP_2. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P. horikoshii inferred from complete genomic sequences."
      Maeder D.L., Weiss R.B., Dunn D.M., Cherry J.L., Gonzalez J.M., DiRuggiero J., Robb F.T.
      Genetics 152:1299-1305(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.
    2. "Methionine aminopeptidase from the hyperthermophilic Archaeon Pyrococcus furiosus: molecular cloning and overexpression in Escherichia coli of the gene, and characteristics of the enzyme."
      Tsunasawa S., Izu Y., Miyagi M., Kato I.
      J. Biochem. 122:843-850(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 1-35, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, MASS SPECTROMETRY.
      Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.
    3. "Overexpression and divalent metal binding properties of the methionyl aminopeptidase from Pyrococcus furiosus."
      Meng L., Ruebush S., D'souza V.M., Copik A.J., Tsunasawa S., Holz R.C.
      Biochemistry 41:7199-7208(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES.
    4. "Crystal structure of methionine aminopeptidase from hyperthermophile, Pyrococcus furiosus."
      Tahirov T.H., Oki H., Tsukihara T., Ogasahara K., Yutani K., Ogata K., Izu Y., Tsunasawa S., Kato I.
      J. Mol. Biol. 284:101-124(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS) IN COMPLEX WITH COBALT, MUTAGENESIS OF HIS-161 AND HIS-173.
    5. "EPR and X-ray crystallographic characterization of the product-bound form of the MnII-loaded methionyl aminopeptidase from Pyrococcus furiosus."
      Copik A.J., Nocek B.P., Swierczek S.I., Ruebush S., Jang S.B., Meng L., D'souza V.M., Peters J.W., Bennett B., Holz R.C.
      Biochemistry 44:121-129(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) IN COMPLEX WITH MANGANESE AND METHIONINE.

    Entry informationi

    Entry nameiMAP2_PYRFU
    AccessioniPrimary (citable) accession number: P56218
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 15, 1998
    Last sequence update: July 15, 1998
    Last modified: May 27, 2015
    This is version 122 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. Peptidase families
      Classification of peptidase families and list of entries
    3. 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.