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(-) Description

Title :  THE X-RAY CRYSTAL STRUCTURE OF MEVALONATE 5-DIPHOSPHATE DECARBOXYLASE AT 2.3 ANGSTROM RESOLUTION.
 
Authors :  J. B. Bonanno, C. Edo, N. Eswar, U. Pieper, M. J. Romanowski, V. Ilyin, S. E. Gerchman, H. Kycia, F. W. Studier, A. Sali, S. K. Burley, New York Research Center For Structural Genomics (Nysgxrc)
Date :  03 Aug 00  (Deposition) - 21 Mar 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.27
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Mixed Alpha/Beta Structure, Atp Binding, Decarboxylase, Cholesterol Biosynthesis, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. B. Bonanno, C. Edo, N. Eswar, U. Pieper, M. J. Romanowski, V. Ilyin, S. E. Gerchman, H. Kycia, F. W. Studier, A. Sali, S. K. Burley
Structural Genomics Of Enzymes Involved In Sterol/Isoprenoi Biosynthesis.
Proc. Natl. Acad. Sci. Usa V. 98 12896 2001
PubMed-ID: 11698677  |  Reference-DOI: 10.1073/PNAS.181466998

(-) Compounds

Molecule 1 - MEVALONATE 5-DIPHOSPHATE DECARBOXYLASE
    ChainsA
    EC Number4.1.1.33
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    MutationYES
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    Other DetailsHIS-TAG MODIFIED PET28A PLASMID
    SynonymMDD, DIPHOSPHOMEVALONATE DECARBOXYLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 9)

Asymmetric Unit (1, 9)
No.NameCountTypeFull Name
1MSE9Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 18)
No.NameCountTypeFull Name
1MSE18Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1FI4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1FI4)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Phe A:268 -Pro A:269

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1FI4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1FI4)

(-) Exons   (1, 1)

Asymmetric Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YNR043W1YNR043W.1XIV:701898-7030881191MVD1_YEAST1-3963961A:3-393391

(-) Sequences/Alignments

Asymmetric 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:391
 aligned with MVD1_YEAST | P32377 from UniProtKB/Swiss-Prot  Length:396

    Alignment length:391
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392 
           MVD1_YEAST     3 VYTASVTAPVNIATLKYWGKRDTKLNLPTNSSISVTLSQDDLRTLTSAATAPEFERDTLWLNGEPHSIDNERTQNCLRDLRQLRKEMESKDASLPTLSQWKLHIVSENNFPTAAGLASSAAGFAALVSAIAKLYQLPQSTSEISRIARKGSGSACRSLFGGYVAWEMGKAEDGHDSMAVQIADSSDWPQMKACVLVVSDIKKDVSSTQGMQLTVATSELFKERIEHVVPKRFEVMRKAIVEKDFATFAKETMMDSNSFHATCLDSFPPIFYMNDTSKRIISWCHTINQFYGETIVAYTFDAGPNAVLYYLAENESKLFAFIYKLFGSVPGWDKKFTTEQLEAFNHQFESSNFTARELDLELQKDVARVILTQVGSGPQETNESLIDAKTGL 393
               SCOP domains d1fi4a1 A:3-190 Mevalonate 5-diphosphate decarboxylase                                                                                                                                      d1fi4a2 A:191-393 Mevalonate 5-diphosphate decarboxylase                                                                                                                                                    SCOP domains
               CATH domains 1fi4A01 A:3-184,A:383-393  [code=3.30.230.10, no name defined]                                                                                                                        1fi4A02 A:185-382  [code=3.30.70.890, no name defined]                                                                                                                                                1fi4A01     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..eeeee....eee....ee...eeeee.......eeeeeee.....................hhhhhhhhhhhhhhhhhh......hhhhh.eeeeeee........hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh..eeeee..........eeeeeehhhhh..eeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh...eeeee.....eeeeee..hhhhhhhhhhhhhh.........hhhhhhhhhhhhhh..........hhhh.eeeeeeee.....ee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:3-393 UniProt: 1-396 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                      Transcript 1
                 1fi4 A   3 VYTASVTAPVNIATLKYWGKRDTKLNLPTNSSISVTLSQDDLRTLTSAATAPEFERDTLWLNGEPHSIDNERTQNCLRDLRQLRKEmESKDASLPTLSQWKLHIVSENNFPTAAGLASSAAGFAALVSAIAKLYQLPQSTSEISRIARKGSGSACRSLFGGYVAWEmGKAEDGHDSmAVQIADSSDWPQmKACVLVVSDIKKDVSSTQGmQLTVATSELFKERIEHVVPKRFEVmRKAIVEKDFATFAKETmmDSNSFHATCLDSFPPIFYmNDTSKRIISWCHTINQFYGETIVAYTFDAGPNAVLYYLAENESKLFAFIYKLFGSVPGWDKKFTTEQLEAFNHQFESSNFTARELDLELQKDVARVILTQVGSGPQETNESLIDAKTGL 393
                                    12        22        32        42        52        62        72        82      | 92       102       112       122       132       142       152       162      |172      |182       192       202       212       222       232    |  242       252 ||    262       272 |     282       292       302       312       322       332       342       352       362       372       382       392 
                                                                                                                 89-MSE                                                                         169-MSE   179-MSE      192-MSE             212-MSE                  237-MSE          254-MSE             274-MSE                                                                                                                   
                                                                                                                                                                                                                                                                                      255-MSE                                                                                                                                      

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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric Unit

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1FI4)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (MVD1_YEAST | P32377)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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.
biological process
    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: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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