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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TUBERCULOSIS DRUG TARGET DECAPRENYL-PHOSPHORYL-BETA-D-RIBOFURANOSE-2-OXIDOREDUCTASE (DPRE1) FROM MYCOBACTERIUM SMEGMATIS
 
Authors :  J. Neres, F. Pojer, E. Molteni, L. R. Chiarelli, N. Dhar, S. Boy-Rottger S. Buroni, E. Fullam, G. Degiacomi, A. Lucarelli, R. J. Read, G. Zanoni D. E. Edmondson, E. De Rossi, M. Pasca, G. Riccardi, A. Mattevi, P. J. D S. T. Cole, C. Binda
Date :  21 May 12  (Deposition) - 05 Sep 12  (Release) - 19 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Tuberculosis, Benzothiazinone, Mycobacteria (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Neres, F. Pojer, E. Molteni, L. R. Chiarelli, N. Dhar, S. Boy-Rottger, S. Buroni, E. Fullam, G. Degiacomi, A. P. Lucarelli, R. J. Read, G. Zanoni, D. E. Edmondson, E. De Rossi, M. R. Pasca, J. D. Mckinney, P. J. Dyson, G. Riccardi, A. Mattevi, S. T. Cole, C. Bind
Structural Basis For Benzothiazinone-Mediated Killing Of Mycobacterium Tuberculosis.
Sci. Transl. Med. V. 4 121 2012
PubMed-ID: 22956199  |  Reference-DOI: 10.1126/SCITRANSLMED.3004395

(-) Compounds

Molecule 1 - DECAPRENYL-PHOSPHORYL-BETA-D-RIBOFURANOSE-2- OXIDOREDUCTASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: MYCOBACTERIUM SMEGMATIS
    Organism Taxid: 1772
    Synonym: OXIDOREDUCTASE, FAD-BINDING

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:24 , ILE A:59 , ALA A:60 , GLY A:62 , LEU A:63 , GLY A:64 , ARG A:65 , SER A:66 , TYR A:67 , ASN A:70 , ALA A:71 , MET A:81 , ALA A:101 , PRO A:123 , GLY A:124 , THR A:125 , VAL A:128 , THR A:129 , GLY A:131 , GLY A:132 , CYS A:136 , ILE A:138 , HIS A:139 , ASN A:185 , GLY A:186 , GLY A:189 , ILE A:191 , LEU A:324 , TYR A:422 , ALA A:424 , HOH A:2009 , HOH A:2017 , HOH A:2095BINDING SITE FOR RESIDUE FAD A 600

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4AUT)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:244 -Pro A:245
2His A:322 -Pro A:323

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_DPRE1_MYCS2_001 *C386GDPRE1_MYCS2  ---  ---AC394G
2UniProtVAR_DPRE1_MYCS2_002 *C386SDPRE1_MYCS2  ---  ---AC394S
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FAD_PCMHPS51387 PCMH-type FAD-binding domain profile.DPRE1_MYCS219-193  1A:27-201

(-) Exons   (0, 0)

(no "Exon" information available for 4AUT)

(-) 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:419
 aligned with DPRE1_MYCS2 | A0R607 from UniProtKB/Swiss-Prot  Length:460

    Alignment length:455
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455     
          DPRE1_MYCS2     6 FPTTTKRLMGWGRTAPTVASVLSTSDPEVIVRAVTRAAEEGGRGVIARGLGRSYGDNAQNGGGLVIDMPALNRIHSIDSGTRLVDVDAGVSLDQLMKAALPHGLWVPVLPGTRQVTVGGAIGCDIHGKNHHSAGSFGNHVRSMELLTANGEVRHLTPAGPDSDLFWATVGGNGLTGIILRATIEMTPTETAYFIADGDVTGSLDETIAFHSDGSEANYTYSSAWFDAISKPPKLGRAAISRGSLAKLDQLPSKLQKDPLKFDAPQLLTLPDIFPNGLANKFTFMPIGELWYRKSGTYRNKVQNLTQFYHPLDMFGEWNRAYGSAGFLQYQFVVPTEAVEEFKSIIVDIQRSGHYSFLNVFKLFGPGNQAPLSFPIPGWNVCVDFPIKAGLHEFVTELDRRVLEFGGRLYTAKDSRTTAETFHAMYPRIDEWIRIRRSVDPDGVFASDMARRLQLL 460
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee........eeeeee...hhhhhhhhhhhhhhhh...eeee...............eeee.hhh..eeeee....eeeee...hhhhhhhhhh...ee..........hhhhhhhh.....hhhhhhhhhh.eeeeeee.....eeee.....hhhhhhhhh.......eeeeeeee.ee....eeeeeeee..hhhhhhhhhhhhhhhhh.eeeeee...........eeeeeeee.hhhhhhhhhhhh....-----------------------------......eeeeeeehhhhhh.......-------..eeeeeeeee..hhhhhhhhhhhhhhhh.....eeeeee.............eeeeeeeee...hhhhhhhhhhhhhhhh..ee.hhhh...hhhhhhhhh.hhhhhhhhhhhhh......hhhhhhh... Sec.struct. author
             SAPs(SNPs) (1) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G-------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S-------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE -------------FAD_PCMH  PDB: A:27-201 UniProt: 19-193                                                                                                                                        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aut A  14 FPTTTKRLMGWGRTAPTVASVLSTSDPEVIVRAVTRAAEEGGRGVIARGLGRSYGDNAQNGGGLVIDMPALNRIHSIDSGTRLVDVDAGVSLDQLMKAALPHGLWVPVLPGTRQVTVGGAIGCDIHGKNHHSAGSFGNHVRSMELLTANGEVRHLTPAGPDSDLFWATVGGNGLTGIILRATIEMTPTETAYFIADGDVTGSLDETIAFHSDGSEANYTYSSAWFDAISKPPKLGRAAISRGSLAKLDQLPSKLQKDPLKF-----------------------------YRKSGTYRNKVQNLTQFYHPLDMFGE-------AGFLQYQFVVPTEAVEEFKSIIVDIQRSGHYSFLNVFKLFGPGNQAPLSFPIPGWNVCVDFPIKAGLHEFVTELDRRVLEFGGRLYTAKDSRTTAETFHAMYPRIDEWIRIRRSVDPDGVFASDMARRLQLL 468
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273|        -         -         -|      313       323     |   -   |   343       353       363       373       383       393       403       413       423       433       443       453       463     
                                                                                                                                                                                                                                                                                              274                           304                      329     337
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 4AUT)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AUT)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AUT)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DPRE1_MYCS2 | A0R607)
molecular function
    GO:0003885    D-arabinono-1,4-lactone oxidase activity    Catalysis of the reaction: D-arabinono-1,4-lactone + O(2) = dehydro-D-arabinono-1,4-lactone + H(2)O(2) + H(+).
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    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:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016614    oxidoreductase activity, acting on CH-OH group of donors    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group act as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
biological process
    GO:0045227    capsule polysaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of polysaccharides that make up the capsule, a protective structure surrounding some species of bacteria and fungi.
    GO:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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  4aut
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 Related Entries

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

UniProtKB/Swiss-Prot
        DPRE1_MYCS2 | A0R607: 4f4q 4g3t 4g3u

(-) Related Entries Specified in the PDB File

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