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(-) Description

Title :  MUS MUSCULUS MEVALONATE PYROPHOSPHATE DECARBOXYLASE
 
Authors :  J. R. Walker, T. Davis, A. Vesterberg, Y. Li, C. Bountra, J. Weigelt, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, S. Dhe-Paganon, Structural Genomics Consortium (Sgc)
Date :  25 Oct 08  (Deposition) - 25 Nov 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cholesterol Biosynthesis, Lipid Synthesis, Lyase, Steroid Biosynthesis, Sterol Biosynthesis, Structural Genomics, Structural Genomics Consortium, Sgc; (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. R. Walker, T. Davis, A. Vesterberg, Y. Li, C. Bountra, J. Weigelt, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, S. Dhe-Paganon
Structure Of Mus Musculus Mevalonate Pyrophosphate Decarboxylase
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MEVALONATE PYROPHOSPHATE DECARBOXYLASE
    ChainsA, B
    EC Number4.1.1.33
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28-MHL
    Expression System StrainBL21(DE3)V2R
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneMVD
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymDIPHOSPHOMEVALONATE DECARBOXYLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:23 , LYS A:26 , ARG A:78 , SER A:156 , GLY A:157 , THR A:212 , MET A:215 , HOH A:402 , HOH A:404 , HOH A:600BINDING SITE FOR RESIDUE PO4 A 401
2AC2SOFTWARETYR B:23 , LYS B:26 , ARG B:78 , SER B:156 , GLY B:157 , THR B:212 , HOH B:485 , HOH B:624 , HOH B:625BINDING SITE FOR RESIDUE PO4 B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3F0N)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe A:271 -Pro A:272
2Phe B:271 -Pro B:272

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3F0N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3F0N)

(-) Exons   (0, 0)

(no "Exon" information available for 3F0N)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:387
 aligned with MVD1_MOUSE | Q99JF5 from UniProtKB/Swiss-Prot  Length:401

    Alignment length:397
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       
           MVD1_MOUSE     2 ASEKPQDLMVTCTAPVNIAVIKYWGKRDEALILPINSSLSVTLHQDQLKTTTTVAISKDFTEDRIWLNGREEDVGQPRLQACLREIRRLARKRRSTEDGDTLPLSLSYKVHVASVNNFPTAAGLASSAAGYACLAYTLAQVYGVEGDLSEVARRGSGSACRSLYGGFVEWQMGEQADGKDSIARQIAPEWHWPQLRILILVVSADKKQTGSTVGMQTSVETSTLLKFRAESVVPERMKEMTRCIQEQDFQGFAQLTMKDSNQFHATCLDTFPPISYLNDTSRRIIQLVHRFNTHQGQTKVAYTFDAGPNAVIFTLEDTVAEFVAAVRHSFPPAANGDKFLKGLQVAPVLLSDELKAALAVEPSPGGVQYIIATQVGPGPQVLDDTHDHLLGQDGLPQ 398
               SCOP domains d3f0na1 A:-3-193 automated matches                                                                                                                                                               d3f0na2 A:19 4-397 automated matches                                                                                                                                                                         SCOP domains
               CATH domains 3f0nA01 A:-3-187,A:383-397  [code=3.30.230.10, no name defined]                                                                                                                            ------------------ ---------------------------------------------------------------------------------------------------------------------------------  ---------------------------------------------3f0nA01         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeee..eeeee....eee....ee...eeeee.......eeeeeee.......eeee..eee...hhhhhhhhhhhhhhhhh-------.hhhhhhhh.eeeeeee..hhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..eeee............eeeee.......eeeeeeee...-...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh...eeee......eeeeee..hhhhhhhhhhhhh.....--..eee........hhhhhhhh........eeeeeeee.....eee.hhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f0n A  -3 RENLYFDLMVTCTAPVNIAVIKYWGKRDEALILPINSSLSVTLHQDQLKTTTTVAISKDFTEDRIWLNGREEDVGQPRLQACLREIRRLARK-------DTLPLSLSYKVHVASVNNFPTAAGLASSAAGYACLAYTLAQVYGVEGDLSEVARRGSGSACRSLYGGFVEWQMGEQADGKDSIARQIAPEWHWPQLRILILVVSAD-KQTGSTVGMQTSVETSTLLKFRAESVVPERMKEMTRCIQEQDFQGFAQLTMKDSNQFHATCLDTFPPISYLNDTSRRIIQLVHRFNTHHGQTKVAYTFDAGPNAVIFTLEDTVAEFVAAVRHSFPPAAN--KFLKGLQVAPVLLSDELKAALVVEPSPGGVQYIIATQVGPGPQVLDDTHDHLLGQDGLPQ 397
                                 || 10        20        30        40        50        60        70        80        90 |     100       110       120       130       140       150       160       170       180       190       200    | |210       220       230       240       250       260       270       280       290       300       310       320       330    |  340       350       360       370       380       390       
                                 2|                                                                                   92     100                                                                                                      205 |                                                                                                                             335  |                                                           
                                  7                                                                                                                                                                                                     207                                                                                                                                338                                                           

Chain B from PDB  Type:PROTEIN  Length:373
 aligned with MVD1_MOUSE | Q99JF5 from UniProtKB/Swiss-Prot  Length:401

    Alignment length:391
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397 
           MVD1_MOUSE     8 DLMVTCTAPVNIAVIKYWGKRDEALILPINSSLSVTLHQDQLKTTTTVAISKDFTEDRIWLNGREEDVGQPRLQACLREIRRLARKRRSTEDGDTLPLSLSYKVHVASVNNFPTAAGLASSAAGYACLAYTLAQVYGVEGDLSEVARRGSGSACRSLYGGFVEWQMGEQADGKDSIARQIAPEWHWPQLRILILVVSADKKQTGSTVGMQTSVETSTLLKFRAESVVPERMKEMTRCIQEQDFQGFAQLTMKDSNQFHATCLDTFPPISYLNDTSRRIIQLVHRFNTHQGQTKVAYTFDAGPNAVIFTLEDTVAEFVAAVRHSFPPAANGDKFLKGLQVAPVLLSDELKAALAVEPSPGGVQYIIATQVGPGPQVLDDTHDHLLGQDGLPQ 398
               SCOP domains d3f0nb1 B:7-193 automated matches                                                                                                                                                          d3f0nb2 B:194-397 automated matches                                                                                                                                                                          SCOP domains
               CATH domains 3f0nB01 B:7-187,B:383-397  [code=3.30.230.10, no name defined]                                                                                                                       ----------------------------------------------------------------------------------------------------------------------------------------------------  ----------------------  ---------------------3f0nB01         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..eeeee....eee....ee...eeeee.......eeeeeeee......eeee..eee...hhhhhhhhhhhhhhhhhhh---------hhhhheeeeeeee...-----hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..eeee............eeeee.......eeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh...eeeee.....eeeeee..hhhhhhhhhhhhh.....--..eee........hhhhhhhh.--.....eeeeeeee.....ee................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f0n B   7 DLMVTCTAPVNIAVIKYWGKRDEALILPINSSLSVTLHQDQLKTTTTVAISKDFTEDRIWLNGREEDVGQPRLQACLREIRRLARKRR---------LSLSYKVHVASVNNFP-----ASSAAGYACLAYTLAQVYGVEGDLSEVARRGSGSACRSLYGGFVEWQMGEQADGKDSIARQIAPEWHWPQLRILILVVSADKKQTGSTVGMQTSVETSTLLKFRAESVVPERMKEMTRCIQEQDFQGFAQLTMKDSNQFHATCLDTFPPISYLNDTSRRIIQLVHRFNTHHGQTKVAYTFDAGPNAVIFTLEDTVAEFVAAVRHSFPPAAN--KFLKGLQVAPVLLSDELKAALV--PSPGGVQYIIATQVGPGPQVLDDTHDHLLGQDGLPQ 397
                                    16        26        36        46        56        66        76        86       | -       106       116  |    126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326        |- |     346       356  |  | 366       376       386       396 
                                                                                                                  94       104            119   125                                                                                                                                                                                                               335  |                  359  |                                   
                                                                                                                                                                                                                                                                                                                                                                     338                     362                                   

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3F0N)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MVD1_MOUSE | Q99JF5)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0030544    Hsp70 protein binding    Interacting selectively and non-covalently with Hsp70 proteins, any of a group of heat shock proteins around 70kDa in size.
    GO:0016831    carboxy-lyase activity    Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
    GO:0004163    diphosphomevalonate decarboxylase activity    Catalysis of the reaction: (R)-5-diphosphomevalonate + ATP = ADP + CO(2) + H(+) + isopentenyl diphosphate + phosphate.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0006695    cholesterol biosynthetic process    The chemical reactions and pathways resulting in the formation of cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones.
    GO:0008203    cholesterol metabolic process    The chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. It is a component of the plasma membrane lipid bilayer and of plasma lipoproteins and can be found in all animal tissues.
    GO:0019287    isopentenyl diphosphate biosynthetic process, mevalonate pathway    The chemical reactions and pathways resulting in the formation of isopentenyl diphosphate, via the intermediate mevalonate. This pathway converts acetate, in the form of acetyl-CoA, to isopentenyl diphosphate (IPP), the fundamental unit in isoprenoid biosynthesis, through a series of mevalonate intermediates.
    GO:0008299    isoprenoid biosynthetic process    The chemical reactions and pathways resulting in the formation of any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0006694    steroid biosynthetic process    The chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification.
    GO:0008202    steroid metabolic process    The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
    GO:0016126    sterol biosynthetic process    The chemical reactions and pathways resulting in the formation of sterols, steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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