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(-) Description

Title :  CRYSTAL STRUCTURE OF STAPHYLOCOCCUS EPIDERMIDIS MEVALONATE DIPHOSPHATE DECARBOXYLASE
 
Authors :  M. L. Barta, A. D. Skaff, W. J. Mcwhorter, H. M. Miziorko, B. V. Geisbrech
Date :  22 Feb 11  (Deposition) - 11 May 11  (Release) - 23 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ghmp Kinase Family, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. L. Barta, D. A. Skaff, W. J. Mcwhorter, T. J. Herdendorf, H. M. Miziorko, B. V. Geisbrecht
Crystal Structures Of Staphylococcus Epidermidis Mevalonate Diphosphate Decarboxylase Bound To Inhibitory Analogs Revea New Insight Into Substrate Binding And Catalysis.
J. Biol. Chem. V. 286 23900 2011
PubMed-ID: 21561869  |  Reference-DOI: 10.1074/JBC.M111.242016

(-) Compounds

Molecule 1 - MEVALONATE DIPHOSPHATE DECARBOXYLASE
    Chains: A, B
    EC Number: 4.1.1.33
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: MVAD
    Organism Scientific: STAPHYLOCOCCUS EPIDERMIDIS
    Organism Taxid: 1282
    Synonym: DIPHOSPHOMEVALONATE DECARBOXYLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3QT5)

(-) Sites  (0, 0)

(no "Site" information available for 3QT5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QT5)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gln A:251 -Pro A:252
2Gln B:251 -Pro B:252

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QT5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3QT5)

(-) Exons   (0, 0)

(no "Exon" information available for 3QT5)

(-) 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:327
 aligned with Q9FD73_STAEP | Q9FD73 from UniProtKB/TrEMBL  Length:327

    Alignment length:329
                              1                                                                                                                                                                                                                                                                                                                                      
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318         
         Q9FD73_STAEP     - --MVKSGKARAHTNIALIKYWGKADETYIIPMNNSLSVTLDRFYTETKVTFDPDFTEDCLILNGNEVNAKEKEKIQNYMNIVRDLAGNRLHARIESENYVPTAAGLASSASAYAALAAACNEALSLNLSDTDLSRLARRGSGSASRSIFGGFAEWEKGHDDLTSYAHGINSNGWEKDLSMIFVVINNQSKKVSSRSGMSLTRDTSRFYQYWLDHVDEDLNEAKEAVKNQDFQRLGEVIEANGLRMHATNLGAQPPFTYLVQESYDAMAIVEQCRKANLPCYFTMDAGPNVKVLVEKKNKQAVMEQFLKVFDESKIIASDIISSGVEIIK 327
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeeeeee....eee....ee...eeeeeeeeeeeeeeeeee......eeee..ee.hhhhhhhhhhhhhhhhhhhh...eeeeeeeee.hhhhh..hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..eeeee........eeeee...hhhh.eeeeee........--hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh...eeee......eeeeeehhhhhhhhhhhhh..hhh.eeeee......ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qt5 A  -1 GSMVKSGKARAHTNIALIKYWGKADETYIIPMNNSLSVTLDRFYTETKVTFDPDFTEDCLILNGNEVNAKEKEKIQNYMNIVRDLAGNRLHARIESENYVPTAAGLASSASAYAALAAACNEALSLNLSDTDLSRLARRGSGSASRSIFGGFAEWEKGHDDLTSYAHGINSNGWEKDLSMIFVVINNQSKK--SRSGMSLTRDTSRFYQYWLDHVDEDLNEAKEAVKNQDFQRLGEVIEANGLRMHATNLGAQPPFTYLVQESYDAMAIVEQCRKANLPCYFTMDAGPNVKVLVEKKNKQAVMEQFLKVFDESKIIASDIISSGVEIIK 327
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188|  |   198       208       218       228       238       248       258       268       278       288       298       308       318         
                                                                                                                                                                                                                        189  |                                                                                                                                       
                                                                                                                                                                                                                           192                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:322
 aligned with Q9FD73_STAEP | Q9FD73 from UniProtKB/TrEMBL  Length:327

    Alignment length:326
                                    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      
         Q9FD73_STAEP     2 VKSGKARAHTNIALIKYWGKADETYIIPMNNSLSVTLDRFYTETKVTFDPDFTEDCLILNGNEVNAKEKEKIQNYMNIVRDLAGNRLHARIESENYVPTAAGLASSASAYAALAAACNEALSLNLSDTDLSRLARRGSGSASRSIFGGFAEWEKGHDDLTSYAHGINSNGWEKDLSMIFVVINNQSKKVSSRSGMSLTRDTSRFYQYWLDHVDEDLNEAKEAVKNQDFQRLGEVIEANGLRMHATNLGAQPPFTYLVQESYDAMAIVEQCRKANLPCYFTMDAGPNVKVLVEKKNKQAVMEQFLKVFDESKIIASDIISSGVEIIK 327
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------GHMP_kinases_N-3qt5B01 B:91-150                             --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------GHMP_kinases_N-3qt5B02 B:91-150                             --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .eeeeeeeeeeeeee....eee....ee...eeeeeeeeeeeeeeeee.......eeee..ee.hhhhhhhhhhhhhhhhhhhh....eeeeeeee........hhhhhhhhhhhhhhhhh....hhhhhhhhhhh.hhhhhhhhh..eeeee........eeeee...hhhh.eeeeee.........----hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh...eeee......eeeeeehhhhhhhhhhhhh..hhh.eeeee......ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qt5 B   2 VKSGKARAHTNIALIKYWGKADETYIIPMNNSLSVTLDRFYTETKVTFDPDFTEDCLILNGNEVNAKEKEKIQNYMNIVRDLAGNRLHARIESENYVPTAAGLASSASAYAALAAACNEALSLNLSDTDLSRLARRGSGSASRSIFGGFAEWEKGHDDLTSYAHGINSNGWEKDLSMIFVVINNQSKKV----GMSLTRDTSRFYQYWLDHVDEDLNEAKEAVKNQDFQRLGEVIEANGLRMHATNLGAQPPFTYLVQESYDAMAIVEQCRKANLPCYFTMDAGPNVKVLVEKKNKQAVMEQFLKVFDESKIIASDIISSGVEIIK 327
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181        |-   |   201       211       221       231       241       251       261       271       281       291       301       311       321      
                                                                                                                                                                                                                      190  195
   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  (0, 0)

(no "SCOP Domain" information available for 3QT5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QT5)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: S5 (103)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9FD73_STAEP | Q9FD73)
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.
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.
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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  Cis Peptide Bonds
    Gln A:251 - Pro A:252   [ RasMol ]  
    Gln B:251 - Pro B:252   [ RasMol ]  
 

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q9FD73_STAEP | Q9FD73: 3qt6 3qt7 3qt8 4dpt 4dpu 4dpw 4dpx 4dpy 4du7 4du8

(-) Related Entries Specified in the PDB File

3qt6 STAPHYLOCOCCUS EPIDERMIDIS MEVALONATE DIPHOSPHATE DECARBOXYLASE COMPLEXED WITH INHIBITOR DPGP
3qt7 STAPHYLOCOCCUS EPIDERMIDIS MEVALONATE DIPHOSPHATE DECARBOXYLASE COMPLEXED WITH INHIBITOR 6-FMVAPP
3qt8 S192A STAPHYLOCOCCUS EPIDERMIDIS MEVALONATE DIPHOSPHATE DECARBOXYLASE COMPLEXED WITH INHIBITOR 6-FMVAPP