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Protein

Diphosphomevalonate decarboxylase

Gene

MVD

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

Functioni

Performs the first committed step in the biosynthesis of isoprenes.

Catalytic activityi

ATP + (R)-5-diphosphomevalonate = ADP + phosphate + isopentenyl diphosphate + CO2.1 Publication

Kineticsi

  1. KM=7.4 µM for (R)-5-diphosphomevalonate1 Publication
  2. KM=0.32 mM for ATP1 Publication

    Pathway:icholesterol biosynthesis

    This protein is involved in the pathway cholesterol biosynthesis, which is part of Steroid biosynthesis.
    View all proteins of this organism that are known to be involved in the pathway cholesterol biosynthesis and in Steroid biosynthesis.

    GO - Molecular functioni

    • ATP binding Source: UniProtKB-KW
    • diphosphomevalonate decarboxylase activity Source: UniProtKB
    • Hsp70 protein binding Source: UniProtKB
    • protein homodimerization activity Source: UniProtKB

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Lyase

    Keywords - Biological processi

    Cholesterol biosynthesis, Cholesterol metabolism, Lipid biosynthesis, Lipid metabolism, Steroid biosynthesis, Steroid metabolism, Sterol biosynthesis, Sterol metabolism

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciMetaCyc:ENSG00000167508-MONOMER.
    BRENDAi4.1.1.33. 2681.
    ReactomeiREACT_147904. Activation of gene expression by SREBF (SREBP).
    REACT_22230. Synthesis of Dolichyl-phosphate.
    REACT_9405. Cholesterol biosynthesis.
    SABIO-RKP53602.
    UniPathwayiUPA00063.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Diphosphomevalonate decarboxylase (EC:4.1.1.33)
    Alternative name(s):
    Mevalonate (diphospho)decarboxylase
    Short name:
    MDDase
    Mevalonate pyrophosphate decarboxylase
    Gene namesi
    Name:MVD
    Synonyms:MPD
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640 Componenti: Chromosome 16

    Organism-specific databases

    HGNCiHGNC:7529. MVD.

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: UniProtKB
    Complete GO annotation...

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi17 – 171N → A: 15-fold inflation in K(m) for mevalonate diphosphate. 1 Publication
    Mutagenesisi161 – 1611R → Q: 1000-fold diminution in specific activity. 1 Publication

    Organism-specific databases

    PharmGKBiPA31330.

    Polymorphism and mutation databases

    BioMutaiMVD.
    DMDMi1706681.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed2 Publications
    Chaini2 – 400399Diphosphomevalonate decarboxylasePRO_0000087012Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei2 – 21N-acetylalanine2 Publications
    Modified residuei96 – 961Phosphoserine2 Publications

    Keywords - PTMi

    Acetylation, Phosphoprotein

    Proteomic databases

    MaxQBiP53602.
    PaxDbiP53602.
    PRIDEiP53602.

    PTM databases

    PhosphoSiteiP53602.

    Expressioni

    Tissue specificityi

    Expressed in heart, skeletal muscle, lung, liver, brain, pancreas, kidney and placenta.1 Publication

    Gene expression databases

    BgeeiP53602.
    CleanExiHS_MVD.
    ExpressionAtlasiP53602. baseline and differential.
    GenevisibleiP53602. HS.

    Organism-specific databases

    HPAiHPA041404.
    HPA048250.

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Protein-protein interaction databases

    BioGridi110682. 26 interactions.
    IntActiP53602. 3 interactions.
    MINTiMINT-5004338.
    STRINGi9606.ENSP00000301012.

    Structurei

    Secondary structure

    1
    400
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi10 – 145Combined sources
    Beta strandi17 – 215Combined sources
    Beta strandi26 – 283Combined sources
    Turni29 – 324Combined sources
    Beta strandi33 – 364Combined sources
    Beta strandi38 – 436Combined sources
    Turni45 – 473Combined sources
    Beta strandi50 – 567Combined sources
    Beta strandi64 – 674Combined sources
    Helixi77 – 8812Combined sources
    Beta strandi110 – 1189Combined sources
    Turni120 – 1223Combined sources
    Helixi126 – 13914Combined sources
    Turni140 – 1434Combined sources
    Helixi149 – 1557Combined sources
    Helixi157 – 1637Combined sources
    Beta strandi164 – 1707Combined sources
    Beta strandi178 – 1803Combined sources
    Beta strandi183 – 1875Combined sources
    Helixi189 – 1913Combined sources
    Beta strandi195 – 2028Combined sources
    Helixi211 – 22111Combined sources
    Helixi223 – 2319Combined sources
    Helixi233 – 24513Combined sources
    Helixi249 – 26820Combined sources
    Beta strandi270 – 2723Combined sources
    Helixi279 – 29517Combined sources
    Beta strandi300 – 3034Combined sources
    Beta strandi306 – 3083Combined sources
    Beta strandi310 – 3156Combined sources
    Helixi316 – 3183Combined sources
    Helixi319 – 32911Combined sources
    Turni337 – 3393Combined sources
    Beta strandi340 – 3434Combined sources
    Helixi352 – 3587Combined sources
    Beta strandi366 – 37510Combined sources
    Helixi385 – 3873Combined sources
    Beta strandi392 – 3943Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3D4JX-ray2.40A/B1-400[»]
    ProteinModelPortaliP53602.
    SMRiP53602. Positions 8-396.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP53602.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG3407.
    GeneTreeiENSGT00390000015359.
    HOVERGENiHBG051503.
    InParanoidiP53602.
    KOiK01597.
    OMAiGIECYYT.
    OrthoDBiEOG7K0ZCW.
    PhylomeDBiP53602.
    TreeFamiTF105952.

    Family and domain databases

    Gene3Di3.30.230.10. 1 hit.
    3.30.70.890. 1 hit.
    InterProiIPR013750. GHMP_kinase_C_dom.
    IPR006204. GHMP_kinase_N_dom.
    IPR005935. Mev_decarb.
    IPR029765. Mev_diP_decarb.
    IPR020568. Ribosomal_S5_D2-typ_fold.
    IPR014721. Ribosomal_S5_D2-typ_fold_subgr.
    [Graphical view]
    PANTHERiPTHR10977. PTHR10977. 1 hit.
    PfamiPF00288. GHMP_kinases_N. 1 hit.
    [Graphical view]
    PIRSFiPIRSF015950. Mev_P_decrbx. 1 hit.
    SUPFAMiSSF54211. SSF54211. 1 hit.
    SSF55060. SSF55060. 1 hit.
    TIGRFAMsiTIGR01240. mevDPdecarb. 1 hit.

    Sequencei

    Sequence statusi: Complete.

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

    P53602-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MASEKPLAAV TCTAPVNIAV IKYWGKRDEE LVLPINSSLS VTLHQDQLKT
    60 70 80 90 100
    TTTAVISKDF TEDRIWLNGR EEDVGQPRLQ ACLREIRCLA RKRRNSRDGD
    110 120 130 140 150
    PLPSSLSCKV HVASVNNFPT AAGLASSAAG YACLAYTLAR VYGVESDLSE
    160 170 180 190 200
    VARRGSGSAC RSLYGGFVEW QMGEQADGKD SIARQVAPES HWPELRVLIL
    210 220 230 240 250
    VVSAEKKLTG STVGMRASVE TSPLLRFRAE SVVPARMAEM ARCIRERDFP
    260 270 280 290 300
    SFAQLTMKDS NQFHATCLDT FPPISYLNAI SWRIIHLVHR FNAHHGDTKV
    310 320 330 340 350
    AYTFDAGPNA VIFTLDDTVA EFVAAVWHGF PPGSNGDTFL KGLQVRPAPL
    360 370 380 390 400
    SAELQAALAM EPTPGGVKYI IVTQVGPGPQ ILDDPCAHLL GPDGLPKPAA
    Length:400
    Mass (Da):43,405
    Last modified:October 1, 1996 - v1
    Checksum:i3FD4741BCC4B68D8
    GO

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti278 – 2781N → H.
    Corresponds to variant rs34519538 [ dbSNP | Ensembl ].
    VAR_051605

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U49260 mRNA. Translation: AAC50440.1.
    BT006930 mRNA. Translation: AAP35576.1.
    CH471184 Genomic DNA. Translation: EAW66792.1.
    BC000011 mRNA. Translation: AAH00011.1.
    CCDSiCCDS10968.1.
    RefSeqiNP_002452.1. NM_002461.2.
    UniGeneiHs.252457.

    Genome annotation databases

    EnsembliENST00000301012; ENSP00000301012; ENSG00000167508.
    GeneIDi4597.
    KEGGihsa:4597.
    UCSCiuc002flf.1. human.

    Keywords - Coding sequence diversityi

    Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U49260 mRNA. Translation: AAC50440.1.
    BT006930 mRNA. Translation: AAP35576.1.
    CH471184 Genomic DNA. Translation: EAW66792.1.
    BC000011 mRNA. Translation: AAH00011.1.
    CCDSiCCDS10968.1.
    RefSeqiNP_002452.1. NM_002461.2.
    UniGeneiHs.252457.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3D4JX-ray2.40A/B1-400[»]
    ProteinModelPortaliP53602.
    SMRiP53602. Positions 8-396.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi110682. 26 interactions.
    IntActiP53602. 3 interactions.
    MINTiMINT-5004338.
    STRINGi9606.ENSP00000301012.

    Chemistry

    BindingDBiP53602.
    ChEMBLiCHEMBL4340.
    GuidetoPHARMACOLOGYi642.

    PTM databases

    PhosphoSiteiP53602.

    Polymorphism and mutation databases

    BioMutaiMVD.
    DMDMi1706681.

    Proteomic databases

    MaxQBiP53602.
    PaxDbiP53602.
    PRIDEiP53602.

    Protocols and materials databases

    DNASUi4597.
    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsembliENST00000301012; ENSP00000301012; ENSG00000167508.
    GeneIDi4597.
    KEGGihsa:4597.
    UCSCiuc002flf.1. human.

    Organism-specific databases

    CTDi4597.
    GeneCardsiGC16M088718.
    HGNCiHGNC:7529. MVD.
    HPAiHPA041404.
    HPA048250.
    MIMi603236. gene.
    neXtProtiNX_P53602.
    PharmGKBiPA31330.
    GenAtlasiSearch...

    Phylogenomic databases

    eggNOGiCOG3407.
    GeneTreeiENSGT00390000015359.
    HOVERGENiHBG051503.
    InParanoidiP53602.
    KOiK01597.
    OMAiGIECYYT.
    OrthoDBiEOG7K0ZCW.
    PhylomeDBiP53602.
    TreeFamiTF105952.

    Enzyme and pathway databases

    UniPathwayiUPA00063.
    BioCyciMetaCyc:ENSG00000167508-MONOMER.
    BRENDAi4.1.1.33. 2681.
    ReactomeiREACT_147904. Activation of gene expression by SREBF (SREBP).
    REACT_22230. Synthesis of Dolichyl-phosphate.
    REACT_9405. Cholesterol biosynthesis.
    SABIO-RKP53602.

    Miscellaneous databases

    ChiTaRSiMVD. human.
    EvolutionaryTraceiP53602.
    GenomeRNAii4597.
    NextBioi17676.
    PROiP53602.
    SOURCEiSearch...

    Gene expression databases

    BgeeiP53602.
    CleanExiHS_MVD.
    ExpressionAtlasiP53602. baseline and differential.
    GenevisibleiP53602. HS.

    Family and domain databases

    Gene3Di3.30.230.10. 1 hit.
    3.30.70.890. 1 hit.
    InterProiIPR013750. GHMP_kinase_C_dom.
    IPR006204. GHMP_kinase_N_dom.
    IPR005935. Mev_decarb.
    IPR029765. Mev_diP_decarb.
    IPR020568. Ribosomal_S5_D2-typ_fold.
    IPR014721. Ribosomal_S5_D2-typ_fold_subgr.
    [Graphical view]
    PANTHERiPTHR10977. PTHR10977. 1 hit.
    PfamiPF00288. GHMP_kinases_N. 1 hit.
    [Graphical view]
    PIRSFiPIRSF015950. Mev_P_decrbx. 1 hit.
    SUPFAMiSSF54211. SSF54211. 1 hit.
    SSF55060. SSF55060. 1 hit.
    TIGRFAMsiTIGR01240. mevDPdecarb. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Molecular cloning and expression of the cDNAs encoding human and yeast mevalonate pyrophosphate decarboxylase."
      Toth M.J., Huwyler L.
      J. Biol. Chem. 271:7895-7898(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], CATALYTIC ACTIVITY, SUBUNIT, TISSUE SPECIFICITY.
      Tissue: Liver.
    2. "Cloning of human full-length CDSs in BD Creator(TM) system donor vector."
      Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S., Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y., Phelan M., Farmer A.
      Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    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: Placenta.
    5. "Post-translational regulation of mevalonate kinase by intermediates of the cholesterol and nonsterol isoprene biosynthetic pathways."
      Hinson D.D., Chambliss K.L., Toth M.J., Tanaka R.D., Gibson K.M.
      J. Lipid Res. 38:2216-2223(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: BIOPHYSICOCHEMICAL PROPERTIES.
    6. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-96, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Cervix carcinoma.
    7. "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
      Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
      Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS].
    8. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    9. "Comparative large-scale characterisation of plant vs. mammal proteins reveals similar and idiosyncratic N-alpha acetylation features."
      Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T., Giglione C.
      Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS].
    10. "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome."
      Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D., Wang L., Ye M., Zou H.
      J. Proteomics 96:253-262(2014) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-96, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Liver.
    11. "Human mevalonate diphosphate decarboxylase: characterization, investigation of the mevalonate diphosphate binding site, and crystal structure."
      Voynova N.E., Fu Z., Battaile K.P., Herdendorf T.J., Kim J.J., Miziorko H.M.
      Arch. Biochem. Biophys. 480:58-67(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS), MUTAGENESIS OF ASN-17 AND ARG-161.

    Entry informationi

    Entry nameiMVD1_HUMAN
    AccessioniPrimary (citable) accession number: P53602
    Secondary accession number(s): Q53Y65
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1996
    Last sequence update: October 1, 1996
    Last modified: July 22, 2015
    This is version 136 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. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    5. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    6. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    7. 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.