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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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei161 – 1611SubstrateUniRule annotation
Metal bindingi178 – 1781Divalent metal cation 1UniRule annotation
Metal bindingi189 – 1891Divalent metal cation 1UniRule annotation
Metal bindingi189 – 1891Divalent metal cation 2; catalyticUniRule annotation
Metal bindingi252 – 2521Divalent metal cation 2; catalytic; via tele nitrogenUniRule annotation
Binding sitei259 – 2591SubstrateUniRule annotation
Metal bindingi284 – 2841Divalent metal cation 2; catalyticUniRule annotation
Metal bindingi315 – 3151Divalent metal cation 1UniRule annotation
Metal bindingi315 – 3151Divalent metal cation 2; catalyticUniRule annotation

GO - Molecular functioni

  1. aminopeptidase activity Source: UniProtKB
  2. metal ion binding Source: UniProtKB-HAMAP
  3. metalloaminopeptidase activity Source: UniProtKB-HAMAP
  4. metalloexopeptidase activity Source: UniProtKB

GO - Biological processi

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

Keywords - Molecular functioni

Aminopeptidase, Hydrolase, Protease

Keywords - Ligandi

Metal-binding

Enzyme and pathway databases

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
ProteomesiUP000005640 Componenti: Chromosome 2

Organism-specific databases

HGNCiHGNC:32583. METAP1D.

Subcellular locationi

  1. Mitochondrion UniRule annotation1 Publication

GO - Cellular componenti

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

Keywords - Cellular componenti

Mitochondrion

Pathology & Biotechi

Polymorphism and mutation databases

BioMutaiMETAP1D.
DMDMi74710242.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 1919MitochondrionUniRule annotationAdd
BLAST
Chaini20 – 335316Methionine aminopeptidase 1D, mitochondrialPRO_0000314126Add
BLAST

Proteomic databases

MaxQBiQ6UB28.
PaxDbiQ6UB28.
PRIDEiQ6UB28.

PTM databases

PhosphoSiteiQ6UB28.

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

BgeeiQ6UB28.
GenevestigatoriQ6UB28.

Organism-specific databases

HPAiHPA030298.
HPA030299.

Interactioni

Protein-protein interaction databases

BioGridi129008. 3 interactions.

Structurei

3D structure databases

ProteinModelPortaliQ6UB28.
SMRiQ6UB28. Positions 63-330.
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

eggNOGiCOG0024.
GeneTreeiENSGT00390000002284.
HOGENOMiHOG000030427.
HOVERGENiHBG067178.
InParanoidiQ6UB28.
KOiK01265.
OMAiLNHIYLH.
OrthoDBiEOG786H38.
PhylomeDBiQ6UB28.
TreeFamiTF325318.

Family and domain databases

Gene3Di3.90.230.10. 1 hit.
HAMAPiMF_01974. MetAP_1.
InterProiIPR001714. Pept_M24_MAP.
IPR000994. Pept_M24_structural-domain.
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 AAY55948.1 differs from that shown. Reason: Erroneous initiation. Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti14 – 141G → V.1 Publication
Corresponds to variant rs10497377 [ dbSNP | Ensembl ].
VAR_050273

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_954697.1. NM_199227.1.
UniGeneiHs.298250.

Genome annotation databases

EnsembliENST00000315796; ENSP00000315152; ENSG00000172878.
GeneIDi254042.
KEGGihsa:254042.
UCSCiuc002uhk.3. human.

Polymorphism and mutation databases

BioMutaiMETAP1D.

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_954697.1. NM_199227.1.
UniGeneiHs.298250.

3D structure databases

ProteinModelPortaliQ6UB28.
SMRiQ6UB28. Positions 63-330.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi129008. 3 interactions.

Protein family/group databases

MEROPSiM24.028.

PTM databases

PhosphoSiteiQ6UB28.

Polymorphism and mutation databases

BioMutaiMETAP1D.
DMDMi74710242.

Proteomic databases

MaxQBiQ6UB28.
PaxDbiQ6UB28.
PRIDEiQ6UB28.

Protocols and materials databases

DNASUi254042.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000315796; ENSP00000315152; ENSG00000172878.
GeneIDi254042.
KEGGihsa:254042.
UCSCiuc002uhk.3. human.

Organism-specific databases

CTDi254042.
GeneCardsiGC02P172865.
HGNCiHGNC:32583. METAP1D.
HPAiHPA030298.
HPA030299.
MIMi610267. gene.
neXtProtiNX_Q6UB28.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiCOG0024.
GeneTreeiENSGT00390000002284.
HOGENOMiHOG000030427.
HOVERGENiHBG067178.
InParanoidiQ6UB28.
KOiK01265.
OMAiLNHIYLH.
OrthoDBiEOG786H38.
PhylomeDBiQ6UB28.
TreeFamiTF325318.

Enzyme and pathway databases

BRENDAi3.4.11.18. 2681.
SABIO-RKQ6UB28.

Miscellaneous databases

ChiTaRSiMETAP1D. human.
GenomeRNAii254042.
NextBioi92234.
PROiQ6UB28.
SOURCEiSearch...

Gene expression databases

BgeeiQ6UB28.
GenevestigatoriQ6UB28.

Family and domain databases

Gene3Di3.90.230.10. 1 hit.
HAMAPiMF_01974. MetAP_1.
InterProiIPR001714. Pept_M24_MAP.
IPR000994. Pept_M24_structural-domain.
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...

Publicationsi

« Hide 'large scale' publications
  1. "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: NUCLEOTIDE SEQUENCE [MRNA], SUBCELLULAR LOCATION.
  2. "MAP1D, a novel methionine aminopeptidase family member is overexpressed in colon cancer."
    Leszczyniecka M., Bhatia U., Cueto M., Nirmala N.R., Towbin H., Vattay A., Wang B., Zabludoff S., Phillips P.E.
    Oncogene 25:3471-3478(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY, VARIANT VAL-14.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. "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].
    Tissue: Brain.
  5. "Kinetic and mutational studies of the number of interacting divalent cations required by bacterial and human methionine aminopeptidases."
    Hu X.V., Chen X., Han K.C., Mildvan A.S., Liu J.O.
    Biochemistry 46:12833-12843(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES.

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: April 29, 2015
This is version 96 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

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.